Hydrophobically-modified hedgehog protein compositions and methods

ABSTRACT

Hydrophobically-modified proteins and methods of making them are described. A hydrophobic moiety is attached to a surface amino acid residue of the protein. The hydrophobic moiety can be a lipid or a peptide. Alternatively, the protein can be derivatized by a wide variety of chemical reactions that append a hydrophobic structure to the protein. The preferred protein is of mammalian origin and is selected from the group consisting of Sonic, Indian, and Desert hedgehog. The hydrophobic moiety is used as a convenient tether to which may be attached a vesicle such as a cell membrane, liposome, or micelle.

RELATED APPLICATIONS

The present application claims priority and is a continuation to PCT Patent Application No. PCT/US98/25676 filed Dec. 3, 1998, and U.S. Provisional applications 60/099,800 (filed Sep. 10, 1998), 60/067,423 (filed Dec. 3, 1997), 60/078,935 (filed Mar. 20, 1998) and 60/089,685 (filed Jun. 17, 1998), the specifications of which are each incorporated by reference herein.

BACKGROUND OF THE INVENTION

It is known that certain proteins exhibit greater biological activity when attached to other moieties, either by formation of multimeric complexes, where the proteins have an opportunity to act in concert, or through other alterations in the protein's physico-chemical properties, such as the protein's absorption, biodistribution and half life. Thus, one current area of research in biotechnology involves the development of methods to modify the physico-chemical properties of proteins so that they can be administered in smaller amounts, with fewer side effects, by new routes, and with less expense.

For example, the binding affinity of any single protein (such as a ligand for its cognate receptor) may be low. However, cells normally express hundreds to thousands of copies of a particular surface receptor, and many receptor-ligand interactions take place simultaneously. When many surface molecules become involved in binding, the total effective affinity is greater than the sum of the binding affinities of the individual molecules. By contrast, when ligand proteins are removed from the cell surface and purified, or isolated by recombinant DNA techniques for use, e.g., as therapeutics, they act as monomers and lose the advantage of acting in concert with many other copies of the same protein associated closely on the surface of a cell. Thus isolated, the low affinity of a protein for its receptor may become a serious drawback to its effectiveness as a therapeutic to block a particular binding pathway, since it must compete against the high avidity cell-cell interactions. Effective treatment might require constant administration and/or high doses. Such drawbacks might be avoided, however, if a means could be found to provide multimeric forms of an isolated protein.

Similarly, it would be useful to modify other physico-chemical properties of biologically active proteins so that, for instance, a protein is induced to associate with a membrane thus localizing it at the site of administration and enhancing its ability to bind to, or otherwise interact with, a particular target. Such changes may also affect the pharmaco-distribution of the protein.

Several methods of generating coupled proteins have been developed. Many of these methods are not highly specific, i.e., they do not direct the point of coupling to any particular site on the protein. As a result, conventional coupling agents may attack functional sites or sterically block active sites, rendering the coupled proteins inactive. Furthermore, the coupled products may be oriented so that the active sites cannot act synergistically, thereby rendering the products no more effective than the monomeric protein alone.

As an additional motivation to find new methods for protein modification, proteins with an N-terminal cysteine residue are susceptible to oxidation or other chemical modifications that may compromise activity or half-life. Additionally, certain buffers commonly used in protein purification have components or impurities that can modify the N-terminal cysteine. Even when these buffers are avoided, the N-terminal cysteine is modified over time, perhaps due to chemicals in the storage vials or in the air. Consequently, formulation buffers must include a protective agent, such as dithiothreitol, to prevent cysteine modification and/or oxidation. However, protective agents have significant biological activity of their own and they may therefore complicate experiments and adversely affect the therapeutic utility of a formulation.

Accordingly, there is a need in the art to develop more specific means to obtain derivatized products or multimeric forms thereof so as to alter the properties of the protein in order to affect its stability, potency, pharmacokinetics, and pharmacodynamics.

SUMMARY OF THE INVENTION

In one aspect of the invention, we have solved the problem of finding a way to conveniently make modified forms of biologically active proteins. Methods of the invention can be used to derive multimeric forms of the proteins and/or can be used to change their physico-chemical properties. We have found that modifying a protein (i.e, adding or appending a hydrophobic moiety to an existing amino acid or substituting a hydrophobic moiety for an amino acid) so as to introduce the hydrophobic moiety onto a protein can increase the protein's biological activity and/or its stability. For example, an N-terminal cysteine can be used as a convenient “target” to attach a hydrophobic moiety (e.g., a lipid) and thereby modify biologically active proteins.

Alternatively, a hydrophobic moiety can be attached to a C-terminal residue of a biologically active protein, such as hedgehog protein, to modify the protein's activity. A hydrophobic moiety can also be appended to an internal amino acid residue to enhance the protein's activity, provided the modification does not affect the activity of the protein, e.g., the proteins ability to bind to a receptor or co-receptor, or affect the protein's 3-dimensional structure. Preferably, the hydrophobic moiety is appended to an internal amino acid residue that is on the surface of the protein when the protein is in its native form. The hydrophobic modification of the invention provides a generically useful method of creating proteins with altered physico-chemical properties as compared to non-modified forms.

This invention originated, at least in part, from the discovery that when we expressed full-length Sonic hedgehog protein in insect and in mammalian cells, the mature form of the protein (residues 1-174 in the mature sequence), in addition to having cholesterol at the C-terminus, is also derivatized at its N-terminal end with a fatty acid. Significantly, this form of hedgehog exhibited about a 30-fold increase in potency as compared to soluble, unmodified hedgehog in an in vitro assay.

One aspect of the invention is therefore an isolated, protein comprising an N-terminal amino acid and a C-terminal amino acid, wherein the protein is selected from the group consisting of a protein with an N-terminal cysteine that is appended with at least one hydrophobic moiety; a protein with an N-terminal amino acid that is not a cysteine appended with a hydrophobic moiety; and a protein with a hydrophobic moiety substituted for the N-terminal amino acid. The hydrophobic moiety can be a hydrophobic peptide or any lipid or any other chemical moiety that is hydrophobic.

The protein may be modified at its N-terminal amino acid and preferably the N-terminal amino acid is a cysteine or a functional derivative thereof. The protein may be modifed at its C-terminal amino acid or at both the N-terminal amino acid and the C-terminal amino acid, or at at least one amino acid internal to (i.e., intermediate between) the N-terminal and C-terminal amino acids, or various combinations of these configurations. The protein can be an extracellular signaling protein and in preferred embodiments, the protein is a hedgehog protein obtainable from a vertebrate source, most preferably obtainable from a human and includes Sonic, Indian, and Desert hedgehog.

Another embodiment is an isolated, protein of the form: A-Cys-[Sp]-B- X, wherein

A is a hydrophobic moiety;

Cys is a cysteine or functional equivalent thereof;

[Sp] is an optional spacer peptide sequence;

B is a protein comprising a plurality of amino acids, including at least one optional spacer peptide sequence; and

X is optionally another hydrophobic moiety linked to the protein.

The isolated protein can be an extracellular signaling protein, preferably a hedgehog protein. This protein can be modified at at least one other amino acid with at least one hydrophobic moiety. In other embodiments, the protein is in contact with a vesicle selected from the group consisting of a cell membrane, micelle and liposome.

Another aspect of the invention is an isolated, protein having a C-terminal amino acid and an N-terminal thiaproline group, the thiaproline group formed by reacting an aldehyde with, e.g., an N-terminal cysteine of the protein. A further aspect of the invention is isolated, protein having a C-terminal amino acid and an N-terminal amide group, the amide group formed by reacting a fatty acid thioester with an N-terminal cysteine of the protein. Yet another aspect of the invention is an isolated, protein having a C-terminal amino acid and an N-terminal maleimide group, the N-terminal maleimide group formed by reacting a maleimide group with the N-terminal cysteine of the protein. Yet another aspect of the invention is an isolated, protein having a C-terminal amino acid and an N-terminal acetamide group. A further aspect of the invention is an isolated, protein having a C-terminal amino acid and an N-terminal thiomorpholine group.

In these embodiments, the C-terminal amino acid of the protein can be modified with an hydrophobic moiety. The isolated protein can be an extracellular signaling protein, most preferably a hedgehog protein.

Methods of the invention include a method of generating a multivalent protein complex comprising the step of linking, in the presence of a vesicle, a hydrophobic moiety to an N-terminal cysteine of a protein, or a functional equivalent of the N-terminal cysteine. The linking step may include linking a lipid moiety which is selected from saturated and unsaturated fatty acids having between 2 and 24 carbon atoms. The protein can be an extracellular signaling protein, preferably a hedgehog protein selected from the group consisting of Sonic, Indian and Desert hedgehog.

Yet another method of the invention is a method for modifying a physico-chemical property of a protein, comprising introducing at least one hydrophobic moiety to an N-terminal cysteine of the protein or to a functional equivalent of the N-terminal cysteine. The hydrophobic moiety can be a lipid moiety selected from saturated and unsaturated fatty acids having between 2 and 24 carbon atoms. It can also be a hydrophobic protein The protein modified using this method can be an extracellular signaling protein, preferably a hedgehog protein selected from the group consisting of Sonic, Indian and Desert hedgehog. Protein complexes produced by these methods are also encompassed by the present invention.

Other extracellular signaling proteins useful in the invention besides hedgehog include gelsolin; an interferon, an interleukin, tumor necrosis factor, monocyte colony stimulating factor, granulocyte colony stimulating factor, granulocyte macrophage colony stimulating factor, erythropoietin, platelet derived growth factor, growth hormone and insulin.

Another method of the invention for modifying a protein (such as an extracellular signaling protein) that has an N-terminal cysteine. This method comprises reacting the N-terminal cysteine with a fatty acid thioester to form an amide, wherein such modification enhances the protein's biological activity.

In a preferred embodiment, the fatty acid thioester is an acylated thiophenol, or active thioester, even more preferably, an acylated thiophenol having at least one electron withdrawing substituent on the phenyl ring of the thiophenol. Suitable electron-withdrawing substituents include nitro, carbonyl (e.g., ester, aldehyde, ketone, amide, carboxyl, or thioester groups), cyano, halogen (preferably chloro or fluoro), sulfonyl (e.g., sulfonamide, sulfonate, sulfonic acid, or sulfone groups), or phosphonyl (e.g., phosphate, phosphate, etc.) groups, preferably nitro, carbonyl, cyano, or halogen groups. Two or more such groups may be present on the phenyl ring. In certain embodiments, the thiophenol may be a polycyclic aromatic thiol, e.g., mercaptonaphthalene, mercaptoanthracene, mercaptofluorene, etc., or a heteroaromatic thiol, e.g., mercaptothiophene, mercaptopyridine, mercaptoindole, mercaptoquinoline, etc.

Yet another method is a method for modifying a protein (such as an extracellular signaling protein) having an N-terminal cysteine, which comprising reacting the N-terminal cysteine with a maleimide group, wherein such modification enhances the protein's biological activity. Other embodiments of this method involve reacting the N-terminal cysteine with either an aldehyde group, an acetamide group or a thiomorpholine group.

A further method is a method for modifying protein (such as an extracellular signaling protein) comprising appending an hydrophobic peptide to the protein. The hydrophobic moiety can be appended to an amino acid of the protein selected from the group consisting of the N-terminal amino acid, the C-terminal amino acid, an amino acid intermediate between the N-terminal amino acid and the C-terminal amino acid, and combinations of the foregoing. In one embodiment, the present invention provides hedgehog polypeptides which are modified with lipophilic moieties. In certain embodiments, the hedgehog proteins of the present invention are modified by a lipophilic moiety or moieties at one or more internal sites of the mature, processed extracellular domain, and may or may not be also derivatized with lipophilic moieties at the N or C-terminal residues of the mature polypeptide. In other embodiments, the polypeptide is modified at the C-terminal residue with a hydrophobic moiety other than a sterol. In still other embodiments, the polypeptide is modified at the N-terminal residue with a cyclic (preferably polycyclic) lipophilic group. Various combinations of the above are also contemplated. A therapeutic method of the invention is a method for treating a neurological disorder in a patient comprising administering to the patient a hydrophobically-modified protein of the invention.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1. Characterization of a palmitoylated form of Shh. A tethered form of human Shh was immunoaffinity purified from High Five™ insect cells and analyzed by SDS-PAGE. The protein was stained with Coomassie blue (lane a, Life Technologies, Inc. prestained high molecular weight markers; lane b, soluble Shh (0.6 μg); lane c, tethered Shh (0.6 μg); lane d, mixture of soluble plus tethered Shh (0.6 μg each)). The ability of Shh and Ihh (see lane h) to be modified with palmitic acid was assayed using a cell-free system described in Example 2. Soluble forms of hedgehog protein (3 μg/sample) were incubated for 1 h with rat liver microsomes, ATP, CoenzymeA, and ³H-palmitic acid, and then analyzed for palmitoylation by SDS-PAGE. The samples shown in lanes e-i were visualized by fluorography (lane e, Shh; lane f, des 1-10 Shh; lane g, Cys-1 to Ser Shh; lane h, Ihh; lane i, His-tagged Shh) and in lanes j-k by Coomassie staining (lane j, Shh; lane k des 1-10 Shh).

FIG. 2. Analysis of purified Shh by ESI-MS. Soluble human Shh (A) and tethered human Shh (B) were analyzed by ESI-MS on a Micromass Quattro II triple quadrupole mass spectrometer, equipped with an electrospray ion source. All electrospray mass spectral data were acquired and stored in profile mode and were processed using the Micromass MassLynx data system. Molecular mass spectra are shown (mass assignments were generated by the data system).

FIG. 3. Analysis of tethered Shh by reverse phase HPLC. Soluble human Shh (A), tethered human Shh from High Five™ insect cells (B), tethered human Shh from EBNA-293 cells (C), and cell-associated rat Shh (D) were subjected to reverse phase HPLC on a narrow bore Vydac C₄ column (2.1 mm internal diameter×250 mm). The column was developed with a 30 min, 0-80% acetonitrile gradient in 0.1% trifluoroacetic acid at 0.25 mL/min and the effluent monitored using a photodiode array detector from 200-300 nm (data shown at 214 nm). Peak fractions were collected and characterized further by SDS-PAGE and MS (data summarized in Tables 3, 4, and 5).

FIG. 4. Characterization of Shh by LC-MS. Tethered human Shh (A) and soluble human Shh (B) were alkylated with 4-vinylpyridine (1 μL/100 μL sample in 6 M guanidine HCl, 1 mM EDTA, 100 mM Tris HCl pH 8.0), ethanol precipitated, and digested with endoproteinase Lys-C in 50 mM Tris HCl pH 7.0, 2 M urea at an enzyme:protein ratio of 1:5 as described previously (27). The digests were analyzed by reverse phase HPLC in line with an electrospray Micromass Quattro II triple quadrupole mass spectrometer. Scans were acquired throughout the run and processed using the Micromass MassLynx data system (total ion chromatograms from the runs are shown). Asterisks indicate the positions of the N-terminal peptide which were verified either by MALDI PSD or N-terminal Edman sequencing.

FIG. 5. Sequencing of the N-terminal Shh peptide by MALDI PSD measurement. The N-terminal endoproteinase Lys-C peptide from tethered human Shh was subjected to MALDI PSD measurement on a Voyager-DE™ STR time of flight mass spectrometer. The predicted fragmentation pattern and nomenclature for the detected fragment ions are shown at the top of the panel (PA, palmitoyl acid; 4vp, 4-pyridylethyl group). The remainder of the Figure shows the molecular mass spectrum produced by the run. Relevant ions are denoted using the nomenclature defined in the schematic. Calculated masses (Da) for b₁-b₈ are 447.3, 504.3, 601.4, 658.4, 814.5, 871.5, 1018.6, and 1075.6, respectively. For y₁-y₈, the masses (Da) are 147.1, 204.1, 351.2, 408.2, 564.3, 621.3, 718.4, and 775.4, respectively. The calculated mass for z₈ is 758.4 Da. The observed mass for b₈ contains an additional 18 Da due to an added water.

FIG. 6. Increased activity of tethered Shh in the C3H10T1/2 assay. The relative potencies of soluble and tethered human Shh lone (A) or in the presence of the anti-hedgehog neutralizing Mab 5E1 (B) where assessed on C3H10T1/2 cells measuring alkaline phosphatase induction. The numbers presented reflect the averages of duplicate determinations. (A) Serial 2-fold dilutions of soluble (circles) and tethered (squares) Shh were incubated with the cells for 5 days and the resulting levels of alkaline phosphatase activity measured at 405 nm using the alkaline phosphatase choromogenic substrate p-nitrophenyl phosphate. (B) Serial dilutions of Mab 5E1 were incubated with soluble Shh (5 μg/mL: black bars) or tethered Shh (0.25 μg/mL: gray bars) or vehicle control without Shh added (white bar) for 30 min and then subjected to analysis in the C3H10T1/2 assay.

FIG. 7. Analysis of Shh in a receptor binding assay. The relative potency of soluble (6) and tethered (8) Shh for binding to patched was assessed on patched-transfected EBNA-293 cells by FACS analysis. Serial dilutions of the test samples were incubated with the EBNA-293 cells, washed, and then the percent binding measured by the ability of the samples to compete with Shh-Ig for binding to the cells. Bound Shh-Ig was quantified by mean fluorescence using a FITC-labeled anti-Ig antibody probe as the readout. The data were fitted to a hyperbolic curve by non-linear regression.

FIG. 8. Alignment of N-terminal fragment of human hedgehog proteins. The 20 kDa human hedgehog proteins (Sonic “Shh”, Desert “Dhh” and Indian “Ihh”) are aligned with respect to their N-terminal cysteine (Cys-1 in the mature sequence). This cysteine is normally Cys-24 in the full-length Shh precursor protein due to the presence of the natural signal sequence that is removed during secretion. The actual position of the cysteine may vary slightly due to species differences.

FIG. 9. Consensus Sequence of the N-terminal fragment of human hedgehog proteins.

FIG. 10. Effect of lipid chain length on activity of human Sonic hedgehog. A series of fatty acid-modified hedgehog proteins was synthesized according to the present invention and the effect of the fatty acid chain length on hedgehog activity was tested using the C3H10T1/2 alkaline phosphatase induction assay described herein. The results are plotted as a bar graph.

FIG. 11. C3H10T1/2 assay of palmitoylated, myristyolated, lauroylated. decanoylated, and octanoylated human Sonic hedgehog. Palmitoylated, lauroylated, decanoylated, and octanoylated human Sonic hedgehog formulated in 5 mM Na₂HPO₄ pH 5.5, 150 mM NaCl, 1% octylglucoside, 0.5 mM DTT, and myristoylated human Sonic hedgehog, formulated in 150 mM NaCl, 0.5 mM DTT, were assayed on C3H10T1/2 cells measuring alkaline phosphatase induction. The numbers represent the mean of duplicate determinations. Serial 3-fold dilutions of palmitoylated (∘), myristoylated (), lauroylated (□), decanoylated (▪), octanoylated (Δ), and unmodified (▾ and X) human Sonic hedgehog were incubated with the cells for 5 days and the resulting levels of alkaline phosphatase measured at 405 nm using the choromogenic substrate p-nitrophenyl phosphate. The palmitoylated, myristoylated, lauroylated, and decanoylated proteins were assayed in one experiment with the unmodified protein shown as (▾), while the octanoylated protein was assayed in another experiment with the unmodified protein shown as (X). The arrow on the y-axis denotes the background level of alkaline phosphatase in the absence of added hedgehog protein.

FIG. 12. Generic structures of various hydrophobically-modified forms of hedgehog. (A) Fatty amide derivative where R=a hydrocarbon chain of a fatty acid; (B) thiazolidine derivative where R=a hydrocarbon; (C) amino acid substitution where R=a hydrophobic amino acid side chain; (D) maleimide derivative where R=a hydrocarbon; (E) SH=free thiol on N-terminal cysteine of wild type hedgehog; (F) an iodoacetamide derivative where R₁=a hydrocarbon and R₂=either H or a hydrocarbon; and (G) thiomorpholinyl derivative where R=a hydrocarbon. For all structures, HH=hedgehog.

FIG. 13. Relative potency of various hydrophobically-modified forms of hedgehog in the C3H10T1/2 assay. The EC₅₀ (2 μg/ml) of unmodified wild type human Sonic hedgehog is designated as 1 X. The potency of the other proteins is expressed as the ratio of the EC₅₀ of wild type protein divided by the EC₅₀ of the modified protein. Modifications are at the N-terminus of the protein unless designated otherwise.

FIG. 14A. Relative potency of the unmodified, myristoylated, octyl maleimide, and C1II mutant of human Sonic hedgehog in a malonate-induced rat striatal lesion assay. The figure shows the reduction in malonate-induced lesion volume which results from the administation of either unmodified, myristoylated, or the C1II mutant of human Sonic hedegehog to the rat striatum.

FIG. 14B. Pretreatment with myristoylated hedgehog protein. This figure is a graph showing the effect of pretreatment with myristoylated Shh in a malonate striatal lesion model

FIG. 15. Specifc activity of modified and unmodified forms of hedgehog protein. This figure illustrates the specific activities of maleimide modified and unmodified hedgehog polypeptides.

DETAILED DESCRIPTION OF THE INVENTION

This invention is based, in part, on the discovery that human Sonic hedgehog, expressed as a full-length construct in either insect or in mammalian cells, has a hydrophobic palmitoyl group appended to the α-amine of the N-terminal cysteine. This is the first example, of which the inventors are aware, of an extracellular signaling protein being modified in such a manner, and, in contrast to thiol-linked palmitic acid modifications whose attachment is readily reversible, this novel N-linked palmitoyl moiety is likely to be very stable by analogy with myristic acid modification.

As a direct consequence of this initial discovery, the inventors have found that increasing the hydrophobic nature of a signaling protein can increase the protein's biological activity. In particular, the inventors have found that appending a hydrophobic moiety to a signaling protein, such as a hedgehog protein, can enhance the protein's activity. The inventors have found that the N-terminal cysteine of biologically active proteins not only provides a convenient site for appending a hydrophobic moiety, and thereby modifying the physico-chemical properties of the protein, but modifications to the N-terminal cysteine can also increase the protein's stability. Additionally, addition of a hydrophobic moiety to an internal amino acid residue on the surface of the protein structure enhances the protein's activity. We use as an example, our discovery of hydrophobic (e.g., lipids and hydrophobic amino acid) modifications of hedgehog protein.

One aspect of the present application is directed to the discovery that, in addition to those effects seen by cholesterol-addition to the C-terminus of extracellular fragments of the protein, at least certain of the biological activities of the hedgehog gene products are unexpectedly potentiated by derivativation of the protein with lipophilic moieties at other sites on the protein and/or by moieties other than cholesterol. Certain aspects of the invention are directed to preparations of hedgehog polypeptides which are modified at sites other than N-terminal or C-terminal residues of the natural processed form of the protein, and/or which are modified at such terminal residues with lipophilic moieties other than a sterol at the C-terminus or fatty acid at the N-terminus.

As described in PCT publications WO 95/18856 and WO 96/17924 (all of which are expressly incorporated by reference herein), hedgehog polypeptides in general are useful in the in vitro and in vivo repairing and/or regulating the functional performance of a wide range of cells, tissues and organs, and have therapeutic uses ragning from neuroprotection, neuroregeneration, enhancement of neural function, regulation of bone and cartilage formation and repair, regulation of spermatogenesis, regulation of lung, liver and other organs arising from the primative gut, regulation of hematopoietic function, etc. Accordingly, the methods and compositions of the present invention include the use of the derivatized hedgehog polypeptides for all such uses as hedgehog proteins have been implicated. Moreover, the subject methods can be performed on cells which are provided in culture (in vitro), or on cells in a whole animal (in vivo).

In one aspect, the present invention provides pharmaceutical preparations comprising, as an active ingredient, a hedgehog polypeptide being derivatized by one or more lipophilic moieties such as described herein.

The subject hedgehog treatments are effective on both human and animal subjects. Animal subjects to which the invention is applicable extend to both domestic animals and livestock, raised either as pets or for commercial purposes. Examples are dogs, cats, cattle, horses, sheep, hogs and goats.

The hedgehog proteins are a family of extracellular signaling proteins that regulate various aspects of embryonic development both in vertebrates and in invertebrates (for reviews see 1,2). The most well-characterized hedgehog protein is Sonic hedgehog (Shh), involved in anterior-posterior patterning, formation of an apical ectodermal ridge, hindgut mesoderm, spinal column, distal limb, rib development, and lung development, and in inducing ventral cell types in the spinal cord, hindbrain and forebrain (3-8). While the mechanism of action of hedgehog proteins is not understood fully, the most recent biochemical and genetic data suggest that the receptor for Shh is the product of the tumor suppressor gene, patched (9,10) and that other proteins; smoothened (10,11), Cubitus interruptus (12,13), and fused (14) are involved in the hedgehog signaling pathway.

Human Shh is synthesized as a 45 kDa precursor protein that is cleaved autocatalytically to yield: (I) a 20 kDa N-terminal fragment that is responsible for all known hedgehog signaling activity (SEQ ID NOS. 1-4); and (II) a 25 kDa C-terminal fragment that contains the autoprocessing activity (15-17). The N-terminal fragment consists of amino acid residues 24-197 of the full-length precursor sequence.

The N-terminal fragment remains membrane-associated through the addition of a cholesterol at its C-terminus (18,19). The addition of the cholesterol is catalyzed by the C-terminal domain during the processing step.

All references cited in the detailed description are, unless otherwise stipulated, incorporated herein by reference.

I. Definitions

The invention will now be described with reference to the following detailed description of which the following definitions are included:

“amino acid”—a monomeric unit of a peptide, polypeptide, or protein. There are twenty amino acids found in naturally occurring peptides, polypeptides and proteins, all of which are L-isomers. The term also includes analogs of the amino acids and D-isomers of the protein amino acids and their analogs.

“protein”—any polymer consisting essentially of any of the 20 amino acids. Although “polypeptide” is often used in reference to relatively large polypeptides, and “peptide” is often used in reference to small polypeptides, usage of these terms in the art overlaps and is varied. The term “protein” as used herein refers to peptides, proteins and polypeptides, unless otherwise noted.

“N-terminal end”—refers to the first amino acid (amino acid number 1) of the mature form of a protein.

“N-terminal cysteine”—refers to the amino acid residue (number 1) as shown in SEQ ID NOS. 1-4. It also refers to any cysteine at position 1 of any other protein, or functional equivalents of this cysteine (See Section IV).

“spacer” sequence refers to a short sequence that can be as small as a single amino acid that may be inserted between an amino acid to be hydrophobically modified (such as, for example, the N-terminal cysteine or functional equivalent) and the remainder of the protein. A spacer is designed to provide separation between the-hydrophobic modification (e.g., the modified N-terminal cysteine) and the rest of the protein so as to prevent the modification from interfering with protein function and/or make it easier for the modification (e.g., the N-terminal cysteine) to link with a lipid, vesicle, or other hydrophobic moiety. Thus, if a protein is modified at its N-terminal cysteine and at an amino acid at another site, there may be two, or more, spacer sequences.

“tethered” protein—refers to a hydrophobically-modified protein according to the invention.

“multivalent protein complex”—refers to a plurality of proteins (i.e., one or more). A lipid or other hydrophobic moiety is attached to at least one of the plurality of proteins. The lipid or other hydrophobic moiety may optionally be in contact with a vesicle. If a protein lacks a lipid or other hydrophobic moiety, then that protein may be cross-linked or bind to a protein that does have a lipid or other hydrophobic moiety. Each protein may be the same or different and each lipid or other hydrophobic moiety may be the same or different.

“vesicle”—refers to any aggregate of lipophilic molecules. The vesicle may be obtained from a biologic source (e.g., a lipid bilayer such as a cell membrane or a cholic acid-derived detergent preparation) or from a non-biologic source (e.g., a non-biologic detergent vesicle as described in Section VI). The shape, type, and configuration of the vesicle is not intended to limit the scope of this invention.

“functional equivalent” of an amino acid residue (e.g., an N-terminal cysteine)—is (i) an amino acid having similar reactive properties as the amino acid residue that was replaced by the functional equivalent; (ii) an amino acid of a ligand of a polypeptide of the invention, the amino acid having similar hydrophobic (e.g., lipid) moiety binding properties as the amino acid residue that was replaced by the functional equivalent; (iii) a non-amino acid molecule having similar hydrophobic (e.g., lipid) moiety binding properties as the amino acid residue that was replaced by the functional equivalent.

“genetic fusion”—refers to a co-linear, covalent linkage of two or more proteins or fragments thereof via their individual peptide backbones, through genetic expression of a polynucleotide molecule encoding those proteins.

A “chimeric protein” or “fusion protein” is a fusion of a first amino acid sequence encoding a hedgehog polypeptide with a second amino acid sequence defining a domain foreign to and not substantially homologous with any domain of hh protein. A chimeric protein may present a foreign domain which is found (albeit in a different protein) in an organism which also expresses the first protein, or it may be an “interspecies”, “intergenic”, etc. fusion of protein structures expressed by different kinds of organisms. In general, a fusion protein can be represented by the general formula (X)_(n)-(hh)_(m)-(Y)_(n), wherein hh represents all or a portion of the hedgehog protein, X and Y each independently represent amino acid sequences which are not naturally found as a polypeptide chain contiguous with the hedgehog sequence, m is an integer greater than or equal to 1, and each occurrence of n is, independently, 0 or an integer greater than or equal to 1 (n and m are preferably no greater than 5 or 10).

“mutant”—any change in the genetic material of an organism, in particular any change (i.e., deletion, substitution, addition, or alteration) in a wild type polynucleotide sequence or any change in a wild type protein.

“wild type”—the naturally-occurring polynucleotide sequence of an exon of a gene encoding a protein, or a portion thereof, or protein sequence, or portion thereof, respectively, as it normally exists in vivo.

“standard hybridization conditions”—salt and temperature conditions substantially equivalent to 0.5×SSC to about 5×SSC and 65° C. for both hybridization and wash. The term “standard hybridization conditions” as used herein is an operational definition and encompasses a range of hybridization conditions. See also Current Protocols in Molecular Biology, John Wiley & Sons, Inc. New York, Sections 6.3.1-6.3.6, (1989).

“expression control sequence”—a sequence of polynucleotides that controls and regulates expression of genes when operatively linked to those genes.

“operatively linked”—a polynucleotide sequence (DNA, RNA) is operatively linked to an expression control sequence when the expression control sequence controls and regulates the transcription and translation of that polynucleotide sequence. The term “operatively linked” includes having an appropriate start signal (e.g., ATG) in front of the polynucleotide sequence to be expressed, and maintaining the correct reading frame to permit expression of the polynucleotide sequence under the control of the expression control sequence, and production of the desired polypeptide encoded by the polynucleotide sequence.

“expression vector”—a polynucleotide, such as a DNA plasmid or phage (among other common examples) which allows expression of at least one gene when the expression vector is introduced into a host cell. The vector may, or may not, be able to replicate in a cell.

“Isolated” (used interchangeably with “substantially pure”)—when applied to nucleic acid i.e., polynucleotide sequences that encode polypeptides, means an RNA or DNA polynucleotide, portion of genomic polynucleotide, cDNA or synthetic polynucleotide which, by virtue of its origin or manipulation: (i) is not associated with all of a polynucleotide with which it is associated in nature (e.g., is present in a host cell as an expression vector, or a portion thereof); or (ii) is linked to a nucleic acid or other chemical moiety other than that to which it is linked in nature; or (iii) does not occur in nature. By “isolated” it is further meant a polynucleotide sequence that is: (i) amplified in vitro by, for example, polymerase chain reaction (PCR); (ii) synthesized chemically; (iii) produced recombinantly by cloning; or (iv) purified, as by cleavage and gel separation.

Thus, “substantially pure nucleic acid” is a nucleic acid which is not immediately contiguous with one or both of the coding sequences with which it is normally contiguous in the naturally occurring genome of the organism from which the nucleic acid is derived. Substantially pure DNA also includes a recombinant DNA which is part of a hybrid gene encoding additional hedgehog sequences.

“Isolated” (used interchangeably with “substantially pure”)—when applied to polypeptides means a polypeptide or a portion thereof which, by virtue of its origin or manipulation: (i) is present in a host cell as the expression product of a portion of an expression vector; or (ii) is linked to a protein or other chemical moiety other than that to which it is linked in nature; or (iii) does not occur in nature, for example, a protein that is chemically manipulated by appending, or adding at least one hydrophobic moiety to the protein so that the protein is in a form not found in nature. By “isolated” it is further meant a protein that is: (i) synthesized chemically; or (ii) expressed in a host cell and purified away from associated and contaminating proteins. The term generally means a polypeptide that has been separated from other proteins and nucleic acids with which it naturally occurs. Preferably, the polypeptide is also separated from substances such as antibodies or gel matrices (polyacrylamide) which are used to purify it.

“Heterologous promoter”—as used herein is a promoter which is not naturally associated with a gene or a purified nucleic acid.

“Homologous”—as used herein is synonymous with the term “identity” and refers to the sequence similarity between two polypeptides, molecules, or between two nucleic acids. When a position in both of the two compared sequences is occupied by the same base or amino acid monomer subunit (for instance, if a position in each of the two DNA molecules is occupied by adenine, or a position in each of two polypeptides is occupied by a lysine), then the respective molecules are homologous at that position. The percentage homology between two sequences is a function of the number of matching or homologous positions shared by the two sequences divided by the number of positions compared×100. For instance, if 6 of 10 of the positions in two sequences are matched or are homologous, then the two sequences are 60% homologous. By way of example, the DNA sequences CTGACT and CAGGTT share 50% homology (3 of the 6 total positions are matched). Generally, a comparison is made when two sequences are aligned to give maximum homology. Such alignment can be provided using, for instance, the method of Needleman et al., J. Mol Biol. 48: 443-453 (1970), implemented conveniently by computer programs such as the Align program (DNAstar, Inc.). Homologous sequences share identical or similar amino acid residues, where similar residues are conservative substitutions for, or “allowed point mutations” of, corresponding amino acid residues in an aligned reference sequence. In this regard, a “conservative substitution” of a residue in a reference sequence are those substitutions that are physically or functionally similar to the corresponding reference residues, e.g., that have a similar size, shape, electric charge, chemical properties, including the ability to form covalent or hydrogen bonds, or the like. Particularly preferred conservative substitutions are those fulfilling the criteria defined for an “accepted point mutation” in Dayhoff et al., 5: Atlas of Protein Sequence and Structure, 5: Suppl. 3, chapter 22: 354-352, Nat. Biomed. Res. Foundation, Washington, D.C. (1978).

In particular, the term “percent identical” refers to sequence identity between two amino acid sequences or between two nucleotide sequences. Identity can each be determined by comparing a position in each sequence which may be aligned for purposes of comparison. When an equivalent position in the compared sequences is occupied by the same base or amino acid, then the molecules are identical at that position; when the equivalent site occupied by the same or a similar amino acid residue (e.g., similar in steric and/or electronic nature), then the molecules can be referred to as homologous (similar) at that position. Expression as a percentage of homology/similarity or identity refers to a function of the number of identical or similar amino acids at positions shared by the compared sequences. Various alignment algorithms and/or programs may be used, including FASTA, BLAST or ENTREZ. FASTA and BLAST are available as a part of the GCG sequence analysis package (University of Wisconsin, Madison, Wis.), and can be used with, e.g., default settings. ENTREZ is available through the National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Md. In one embodiment, the percent identity of two sequences can be determined by the GCG program with a gap weight of 1, e.g., each amino acid gap is weighted as if it were a single amino acid or nucleotide mismatch between the two sequences.

A “hedgehog protein” or “hedgehog polypeptide”, as the terms are used interchangeably, of the invention is defined in terms of having at least a portion that includes the consensus amino acid sequence of SEQ ID NO: 4, 15 or 6. The term also means a hedgehog polypeptide, or a functional variant of a hedgehog polypeptide, or homolog of a hedgehog polypeptide, or functional variant, which has biological activity. In particular, the terms encompasses preparations of hedgehog proteins and peptidyl fragments thereof, both agonist and antagonist forms as the specific context will make clear.As used herein the term “bioactive fragment of a hedgehog protein” refers to a fragment of a full-length hedgehog polypeptide, wherein the fragment specifically agonizes or antagonizes inductive events mediated by wild-type hedgehog proteins. The hedgehog biactive fragment preferably is a soluble extracellular portion of a hedgehog protein, where solubility is with reference to physiologically compatible solutions. Exemplary bioactive fragments are described in PCT publications WO 95/18856 and WO 96/17924. In preferred embodiments, the hedgehog polypeptides of the present invention bind to the patched protein, e.g., a protein encoded by GenBank Accession U59464 and described by Johnson et al. (1996) Science 272: 1668.

The term “corresponds to”, when referring to a particular polypeptide or nucleic acid sequence is meant to indicate that the sequence of interest is identical or homologous to the reference sequence to which it is said to correspond.

The terms “peptide(s)”, “protein(s)” and “polypeptide(s)” are used interchangeably herein. The terms “polynucleotide sequence” and “nucleotide sequence” are also used interchangeably herein. The terms “Hedgehog fragment” and “Hedgehog N-terminal fragment” are used interchangeably with “Hedgehog”.

A hedgehog molecule has “biological activity” if it has at least one of the following properties: (i) the molecule meets the hedgehog consensus criteria as defined herein (SEQ ID NO: 4) and has the ability to bind to its receptor, patched; (ii) the molecule meets the hedgehog consensus criteria as defined herein or it encodes, upon expression, a polypeptide that has this characteristic; and (iii) it may induce alkaline phosphatase activity in C3H10T1/2 cells. Generally, any protein has “biological activity” if the protein has in vitro effects, properties, or characteristics that persons having ordinary skill in the art would recognize as being representative of, commensurate with, or reasonably predictive of, the protein's in vivo effects.

The term “hydrophobic” refers to the tendency of chemical moieties with nonpolar atoms to interact with each other rather than water or other polar atoms. Materials that are “hydrophobic” are, for the most part, insoluble in water. Natural products with hydrophobic properties include lipids, fatty acids, phospholipids, sphingolipids, acylglycerols, waxes, sterols, steroids, terpenes, prostaglandins, thromboxanes, leukotrienes, isoprenoids, retenoids, biotin, and hydrophobic amino acids such as tryptophan, phenylalanine, isoleucine, leucine, valine, methionine, alanine, proline, and tyrosine. A chemical moiety is also hydrophobic or has hydrophobic properties if its physical properties are determined by the presence of nonpolar atoms. The term includes lipophilic groups.

The term “lipophilic group”, in the context of being attached to a polypeptide, refers to a group having high hydrocarbon content thereby giving the group high affinity to lipid phases. A lipophilic group can be, for example, a relatively long chain alkyl or cycloalkyl (preferably n-alkyl) group having approximately 7 to 30 carbons. The alkyl group may terminate with a hydroxy or primary amine “tail”. To further illustrate, lipophilic molecules include naturally-occurring and synthetic aromatic and non-aromatic moieties such as fatty acids, esters and alcohols, other lipid molecules, cage structures such as adamantane and buckminsterfullerenes, and aromatic hydrocarbons such as benzene, perylene, phenanthrene, anthracene, naphthalene, pyrene, chrysene, and naphthacene.

The phrase “internal amino acid” means any amino acid in a peptide sequence that is neither the N-terminal amino acid nor the C-terminal amino acid.

The phrase “surface amino acid” means any amino acid that is exposed to solvent when a protein is folded in its native form.

The phrase “extracellular signaling protein” means any protein that is either secreted from a cell, or is tethered to the outside of a cell, and upon binding to the receptor for that protein on a target cell triggers a response in the target cell.

The term “percent identical” refers to sequence identity between two amino acid sequences or between two nucleotide sequences. Identity can each be determined by comparing a position in each sequence which may be aligned for purposes of comparison. When an equivalent position in the compared sequences is occupied by the same base or amino acid, then the molecules are identical at that position; when the equivalent site occupied by the same or a similar amino acid residue (e.g., similar in steric and/or electronic nature), then the molecules can be referred to as homologous (similar) at that position. Expression as a percentage of homology/similarity or identity refers to a function of the number of identical or similar amino acids at positions shared by the compared sequences. Various alignment algorithms and/or programs may be used, including FASTA, BLAST or ENTREZ. FASTA and BLAST are available as a part of the GCG sequence analysis package (University of Wisconsin, Madison, Wis.), and can be used with, e.g., default settings. ENTREZ is available through the National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Md. In one embodiment, the percent identity of two sequences can be determined by the GCG program with a gap weight of 1, e.g., each amino acid gap is weighted as if it were a single amino acid or nucleotide mismatch between the two sequences.

An “effective amount” of, e.g., a hedgehog polypeptide, with respect to the subject methods of treatment, refers to an amount of polypeptide in a preparation which, when applied as part of a desired dosage regimen brings about, e.g., a change in the rate of cell proliferation and/or the state of differentiation of a cell and/or rate of survival of a cell according to clinically acceptable standards for the disorder to be treated or the cosmetic purpose.

A “patient” or “subject” to be treated by the subject method can mean either a human or non-human animal.

The “growth state” of a cell refers to the rate of proliferation of the cell and the state of differentiation of the cell.

Practice of the present invention will employ, unless indicated otherwise, conventional techniques of cell biology, cell culture, molecular biology, microbiology, recombinant DNA, protein chemistry, and immunology, which are within the skill of the art. Such techniques are described in the literature.

II. General Properties of Isolated Hedgehog Proteins

The hedgehog therapeutic compositions of the subject method can be generated by any of a variety of techniques, including purification of naturally occurring proteins, recombinantly produced proteins and synthetic chemistry. Polypeptide forms of the hedgehog therapeutics are preferably derived from vertebrate hedgehog proteins, e.g., have sequences corresponding to naturally occurring hedgehog proteins, or fragments thereof, from vertebrate organisms. However, it will be appreciated that the hedgehog polypeptide can correspond to a hedgehog protein (or fragment thereof) which occurs in any metazoan organism.

Various naturally-occurring hedgehog proteins from which the subject therapeutics can be derived are characterized by a signal peptide, a highly conserved N-terminal region, and a more divergent C-terminal domain. In addition to signal sequence cleavage in the secretory pathway (Lee, J. J. et al. (1992) Cell 71:33-50; Tabata, T. et al. (1992) Genes Dev. 2635-2645; Chang, D. E. et al. (1994) Development 120:3339-3353), hedgehog precursor proteins naturally undergo an internal autoproteolytic cleavage which depends on conserved sequences in the C-terminal portion (Lee et al. (1994) Science 266:1528-1537; Porter et al. (1995) Nature 374:363-366). This autocleavage leads to a 19 kD N-terminal peptide and a C-terminal peptide of 26-28 kD (Lee et al. (1992) supra; Tabata et al. (1992) supra; Chang et al. (1994) supra; Lee et al. (1994) supra; Bumcrot, D. A., et al. (1995) Mol. Cell. Biol. 15:2294-2303; Porter et al. (1995) supra; Ekker, S. C. et al. (1995) Curr. Biol. 5:944-955; Lai, C. J. et al. (1995) Development 121:2349-2360). The N-terminal peptide stays tightly associated with the surface of cells in which it was synthesized, while the C-terminal peptide is freely diffusible both in vitro and in vivo (Lee et al. (1994) supra; Bumcrot et al. (1995) supra; Mart', E. et al. (1995) Development 121:2537-2547; Roelink, H. et al. (1995) Cell 81:445-455). Cell surface retention of the N-terminal peptide is dependent on autocleavage, as a truncated form of hedgehog encoded by an RNA which terminates precisely at the normal position of internal cleavage is diffusible in vitro (Porter et al. (1995) supra) and in vivo (Porter, J. A. et al. (1996) Cell 86, 21-34). Biochemical studies have shown that the autoproteolytic cleavage of the hedgehog precursor protein proceeds through an internal thioester intermediate which subsequently is cleaved in a nucleophilic substitution. It is suggested that the nucleophile is a small lipophilic molecule, more particularly cholesterol, which becomes covalently bound to the C-terminal end of the N-peptide (Porter et al. (1996) supra), tethering it to the cell surface.

TABLE 1 Guide to hedgehog sequences in Sequence Listing Nucleotide Chicken Shh SEQ ID No. 5 Mouse Dhh SEQ ID No. 6 Mouse Ihh SEQ ID No. 7 Mouse Shh SEQ ID No. 8 Zebrafish Shh SEQ ID No. 9 Human Shh SEQ ID No. 10 Human Ihh SEQ ID No. 11 Human Dhh SEQ ID No. 12 Zebrafish Thh SEQ ID No. 13 Drosophila HH SEQ ID No. 14

In addition to the sequence variation between the various hedgehog homologs, the hedgehog proteins are apparently present naturally in a number of different forms, including a pro-form, a full-length mature form, and several processed fragments thereof. The pro-form includes an N-terminal signal peptide for directed secretion of the extracellular domain, while the full-length mature form lacks this signal sequence.

Shh and mouse Ihh genes encode glycoproteins which undergo cleavage, yielding an amino terminal fragment of about 20 kDa (See FIG. 8) and a carboxy terminal fragment of about 25 kDa. The most preferred 20 kDa fragment has the consensus sequence SEQ ID NO: 4, 15 or 16, and more preferably includes the amino acid sequences of SEQ ID NOS: 1-3. Various other fragments that encompass the 20 kDa moiety are considered within the presently claimed invention. Publications disclosing these sequences, as well as their chemical and physical properties, include (34-38); PCT Patent Applications WO 95/23223 (Jessell, Dodd, Roelink and Edlund), WO 95/18856 (Ingham, McMahon and Tabin) and WO 96/17924 (Beachy et al.). Other bioactive fragments of hedgehog polypeptides of the present invention have been generated and are described in great detail in, e.g., PCT publications WO 95/18856 and WO 96/17924.

Moreover, mutagenesis can be used to create modified hh polypeptides, e.g., for such purposes as enhancing therapeutic or prophylactic efficacy, or stability (e.g., ex vivo shelf life and resistance to proteolytic degradation in vivo). Such modified peptides can be produced, for instance, by amino acid substitution, deletion, or addition. Modified hedgehog polypeptides can also include those with altered post-translational processing relative to a naturally occurring hedgehog protein, e.g., altered glycosylation, cholesterolization, prenylation and the like.

In one embodiment, the hedgehog therapeutic is a polypeptide encodable by a nucleotide sequence that hybridizes under stringent conditions to a hedgehog coding sequence represented in one or more of SEQ ID Nos:5-14. Appropriate stringency conditions which promote DNA hybridization, for example, 6.0×sodium chloride/sodium citrate (SSC) at about 45° C., followed by a wash of 2.0×SSC at 50° C., are known to those skilled in the art or can be found in Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6. For example, the salt concentration in the wash step can be selected from a low stringency of about 2.0×SSC at 50° C. to a high stringency of about 0.2×SSC at 50° C. In addition, the temperature in the wash step can be increased from low stringency conditions at room temperature, about 22° C., to high stringency conditions at about 65° C.

As described in the literature, genes for other hedgehog proteins, e.g., from other animals, can be obtained from mRNA or genomic DNA samples using techniques well known in the art. For example, a cDNA encoding a hedgehog protein can be obtained by isolating total mRNA from a cell, e.g. a mammalian cell, e.g. a human cell, including embryonic cells. Double stranded cDNAs can then be prepared from the total mRNA, and subsequently inserted into a suitable plasmid or bacteriophage vector using any one of a number of known techniques. The gene encoding a hedgehog protein can also be cloned using established polymerase chain reaction techniques.

Preferred nucleic acids encode a hedgehog polypeptide comprising an amino acid sequence at least 60% identical, more preferably 70% identical and most preferably 80% identical with an amino acid sequence selected from the group consisting of SEQ ID Nos:1-3. Nucleic acids which encode polypeptides at least about 90%, more preferably at least about 95%, and most preferably at least about 98-99% identity with an amino acid sequence represented in one of SEQ ID Nos:1-3 are also within the scope of the invention.

Family members useful in the methods of the invention include any of the naturally-occurring native hedgehog proteins including allelic, phylogenetic counterparts or other variants thereof, whether naturally-sourced or produced chemically including muteins or mutant proteins, as well as recombinant forms and new, active members of the hedgehog family. Particularly useful hedgehog polypeptides include SEQ ID NOS: 1-4.

Isolated hedgehog polypeptides used in the method of the invention have biological activity. The polypeptides include an amino acid sequence at least 60%, 80%, 90%, 95%, 98%, or 99% homologous to an amino acid sequence from SEQ ID NOS; 1-4. The polypeptide can also include an amino acid sequence essentially the same as an amino acid sequence in SEQ ID NOS: 1-4. The polypeptide is at least 5, 10, 20, 50, 100, or 150 amino acids in length and includes at least 5, preferably at least 10, more preferably at least 20, most preferably at least 50, 100, or 150 contiguous amino acids from SEQ ID NOS: 1-4.

The term “recombinant protein” refers to a polypeptide of the present invention which is produced by recombinant DNA techniques, wherein generally, DNA encoding a hedgehog polypeptide is inserted into a suitable expression vector which is in turn used to transform a host cell to produce the heterologous protein. Moreover, the phrase “derived from”, with respect to a recombinant hedgehog gene, is meant to include within the meaning of “recombinant protein” those proteins having an amino acid sequence of a native hedgehog protein, or an amino acid sequence similar thereto which is generated by mutations including substitutions and deletions (including truncation) of a naturally occurring form of the protein.

As is known in the art, hedgehog polypeptides can be produced by standard biological techniques. For example, a host cell transfected with a nucleic acid vector directing expression of a nucleotide sequence encoding the subject polypeptides can be cultured under appropriate conditions to allow expression of the peptide to occur. The polypeptide hedgehog may be secreted and isolated from a mixture of cells and medium containing the recombinant hedgehog polypeptide. Alternatively, the peptide may be retained cytoplasmically by removing the signal peptide sequence from the recombinant hedgehog gene and the cells harvested, lysed and the protein isolated. A cell culture includes host cells, media and other byproducts. Suitable media for cell culture are well known in the art. The recombinant hedgehog polypeptide can be isolated from cell culture medium, host cells, or both using techniques known in the art for purifying proteins including ion-exchange chromatography, gel filtration chromatography, ultrafiltration, electrophoresis, and immunoaffinity purification with antibodies specific for such peptide. In a preferred embodiment, the recombinant hedgehog polypeptide is a fusion protein containing a domain which facilitates its purification, such as an hedgehog/GST fusion protein. The host cell may be any prokaryotic or eukaryotic cell.

Recombinant hedgehog genes can be produced by ligating nucleic acid encoding an hedgehog protein, or a portion thereof, into a vector suitable for expression in either prokaryotic cells, eukaryotic cells, or both. Expression vectors for production of recombinant forms of the subject hedgehog polypeptides include plasmids and other vectors. For instance, suitable vectors for the expression of a hedgehog polypeptide include plasmids of the types: pBR322-derived plasmids, pEMBL-derived plasmids, pEX-derived plasmids, pBTac-derived plasmids and pUC-derived plasmids for expression in prokaryotic cells, such as E. coli.

A number of vectors exist for the expression of recombinant proteins in yeast. For instance, YEP24, YIP5, YEP51, YEP52, pYES2, and YRP17 are cloning and expression vehicles useful in the introduction of genetic constructs into S. cerevisiae (see, for example, Broach et al. (1983) in Experimental Manipulation of Gene Expression, ed. M. Inouye Academic Press, p. 83, incorporated by reference herein). These vectors can replicate in E. coli due the presence of the pBR322 ori, and in S. cerevisiae due to the replication determinant of the yeast 2 micron plasmid. In addition, drug resistance markers such as ampicillin can be used. In an illustrative embodiment, an hedgehog polypeptide is produced recombinantly utilizing an expression vector generated by sub-cloning the coding sequence of one of the hedgehog genes represented in SEQ ID Nos:1-9 or 19.

The preferred mammalian expression vectors contain both prokaryotic sequences, to facilitate the propagation of the vector in bacteria, and one or more eukaryotic transcription units that are expressed in eukaryotic cells. The pcDNAI/amp, pcDNAI/neo, pRc/CMV, pSV2gpt, pSV2neo, pSV2-dhfr, pTk2, pRSVneo, pMSG, pSVT7, pko-neo and pHyg derived vectors are examples of mammalian expression vectors suitable for transfection of eukaryotic cells. Some of these vectors are modified with sequences from bacterial plasmids, such as pBR322, to facilitate replication and drug resistance selection in both prokaryotic and eukaryotic cells. Alternatively, derivatives of viruses such as the bovine papillomavirus (BPV-1), or Epstein-Barr virus (pHEBo, pREP-derived and p205) can be used for transient expression of proteins in eukaryotic cells. The various methods employed in the preparation of the plasmids and transformation of host organisms are well known in the art. For other suitable expression systems for both prokaryotic and eukaryotic cells, as well as general recombinant procedures, see Molecular Cloning A Laboratory Manual, 2nd Ed., ed. by Sambrook, Fritsch and Maniatis (Cold Spring Harbor Laboratory Press: 1989) Chapters 16 and 17.

In some instances, it may be desirable to express the recombinant hedgehog polypeptide by the use of a baculovirus expression system. Examples of such baculovirus expression systems include pVL-derived vectors (such as pVL1392, pVL1393 and pVL941), pAcUW-derived vectors (such as pAcUWI), and pBlueBac-derived vectors (such as the β-gal containing pBlueBac III).

Alternatively, the coding sequences for the polypeptide can be incorporated as a part of a fusion gene including a nucleotide sequence encoding a different polypeptide. It is widely appreciated that fusion proteins can also facilitate the expression of proteins, and accordingly, can be used in the expression of the hedgehog polypeptides of the present invention. For example, hedgehog polypeptides can be generated as glutathione-S-transferase (GST-fusion) proteins. Such GST-fusion proteins can enable easy purification of the hedgehog polypeptide, as for example by the use of glutathione-derivatized matrices (see, for example, Current Protocols in Molecular Biology, eds. Ausubel et al. (N.Y.: John Wiley & Sons, 1991)). In another embodiment, a fusion gene coding for a purification leader sequence, such as a poly-(His)/enterokinase cleavage site sequence, can be used to replace the signal sequence which naturally occurs at the N-terminus of the hedgehog protein (e.g.of the pro-form, in order to permit purification of the poly(His)-hedgehog protein by affinity chromatography using a Ni²⁺ metal resin. The purification leader sequence can then be subsequently removed by treatment with enterokinase (e.g., see Hochuli et al. (1987) J. Chromatography 411:177; and Janknecht et al. PNAS 88:8972).

In a preferred embodiment, isolated hedgehog is a hedgehog polypeptide with one or more of the following characteristics:

(i) it has at least 30, 40, 42, 50, 60, 70, 80, 90 or 95% sequence identity with amino acids of SEQ ID NOS: 1-4;

(ii) it has a cysteine or a functional equivalent as the N-terminal amino acid;

(iii) it may induce alkaline phosphatase activity in C3H10T1/2 cells;

(iv) it is encodable by a nucleic acid which hybridizes under strignet conditions to a sequence of SEQ ID NO: 5-14;

(v) it can be isolated from natural sources such as mammalian cells;

(vi) it can bind or interact with patched; and

(vii) it is hydrophobically-modified (i.e., it has at least one hydrophobic moiety attached to the polypeptide).

III. Other Proteins

Since techniques exist for engineering a cysteine residue (or its functional equivalent) into a polypeptide's primary sequence, virtually any protein can be converted into a hydrophobically-modified form using the methods described herein.

Viral receptors, cell receptors, and cell ligands are useful because they bind typically to cells or tissues exhibiting many copies of the receptor. Useful viral-cell protein receptors that can be complexed together using the methods of this invention include ICAM1, a rhinovirus receptor; CD2, the Epstein-Barr virus receptor; and CD4, the receptor for human immunodeficiency virus (HIV). Other proteins include members of the cell adhesion molecule family, such as ELAM-1 and VCAM-1 and VCAM-1b and their lymphocyte counterparts (ligands); the lymphocyte associated antigens LFA1, LFA2 (CD2) and LFA3 (CD58), CD59 (a second ligand of CD2), members of the CD11/CD18 family and very late antigens such as VLA4 and their ligands.

Immunogens from a variety of pathogens (e.g., from bacterial, fungal, viral, and other eukaryotic parasites) may also be used as polypeptides in the methods of the invention. Bacterial immunogens include, but are not limited to, bacterial sources responsible for bacterial pneumonia and pneumocystis pneumonia. Parasitic sources include the Plasmodium malaria parasite. Viral sources include poxvirus (e.g, cowpox, herpes simplex, cytomegalovirus); adenoviruses; papovaviruses (e.g., papillomavirus); parvoviruses (e.g., adeno-associated virus); retroviruses (e.g., HTLV I, HTLV II, HIV I and HIV II) and others. Immunoglobulins, or fragments thereof, may also be polypeptides that can be modified according to the invention. One can generate monoclonal Fab fragments recognizing specific antigens using conventional methods (49) and use the individual Fab domains as functional moieties in multimeric constructs according to this invention. Other useful proteins include, gelsolin (50); cytokines, including the various interferons (interferon-α, interferon-β, and interferon-γ); the various interleukins (e.g., IL-1, -2, -3, -4, and the like); the tumor necrosis factors-α and -β; monocyte colony stimulating factor (M-CSF), granulocyte colony stimulating factor (G-CSF), granulocyte macrophage colony stimulating factor (GM-CSF), erythropoietin, platelet-derived growth factor (PDGF), and human and animal hormones, including growth hormone and insulin.

Generally, the structure of the modified proteins of this invention has the general formula: A-Cys-[Sp]-B-[Sp]-X, where A is a hydrophobic moiety; Cys is a cysteine or a functional equivalent thereof; [Sp] is an optional spacer peptide sequence; B is a protein (which optionally may have another spacer peptide sequence as shown); and X is a hydrophobic moiety linked (optionally by way of the spacer peptide) to the a C-terminal end of the protein or another surface site of the protein, wherein the derivatized protein includes at least one of A or X. If X is cholesterol, then B may, or may not be, a hedgehog protein. As discussed above, the purpose of the spacer is to provide separation between the hydrophobic moiety and the rest of the protein so as to make it easier for the hydrophobic moiety (e.g., a modified N-terminal cysteine) to link with another moiety which may be a lipid or a vesicle. The spacer is also intended to make it more difficult for the modification to interfere with protein function. A spacer may be as small as a single amino acid in length. Generally, prolines and glycines are preferred. A particularly preferred spacer sequence is derived from Sonic hedgehog and consists of the amino acid sequence: G-P-G-R.

IV. Production of Recombinant Polypeptides

The isolated polypeptides described herein can be produced by any suitable method known in the art. Such methods range from direct protein synthetic methods to constructing a DNA sequence encoding isolated polypeptide sequences and expressing those sequences in a suitable transformed host.

In one embodiment of a recombinant method, a DNA sequence is constructed by isolating or synthesizing a DNA sequence encoding a wild type protein of interest. Optionally, the sequence may be mutagenized by site-specific mutagenesis to provide functional analogs thereof. See, e.g., (40) and U.S. Pat. No. 4,588,585. Another method of constructing a DNA sequence encoding a polypeptide of interest would be by chemical synthesis using an oligonucleotide synthesizer. Such oligonucleotides may be preferably designed based on the amino acid sequence of the desired polypeptide, and preferably selecting those codons that are favored in the host cell in which the recombinant polypeptide of interest will be produced.

Standard methods may be applied to synthesize an isolated polynucleotide sequence encoding a isolated polypeptide of interest. For example, a complete amino acid sequence may be used to construct a back-translated gene. See Maniatis et al., supra. Further, a DNA oligomer containing a nucleotide sequence coding for the particular isolated polypeptide may be synthesized. For example, several small oligonucleotides coding for portions of the desired polypeptide may be synthesized and then ligated. The individual oligonucleotides typically contain 5′ or 3′ overhangs for complementary assembly.

Once assembled (by synthesis, site-directed mutagenesis, or by another method), the mutant DNA sequences encoding a particular isolated polypeptide of interest will be inserted into an expression vector and operatively linked to an expression control sequence appropriate for expression of the protein in a desired host. Proper assembly may be confirmed by nucleotide sequencing, restriction mapping, and expression of a biologically active polypeptide in a suitable host. As is well known in the art, in order to obtain high expression levels of a transfected gene in a host, the gene must be operatively linked to transcriptional and translational expression control sequences that are functional in the chosen expression host.

The choice of expression control sequence and expression vector will depend upon the choice of host. A wide variety of expression host/vector combinations may be employed. Useful expression vectors for eukaryotic hosts, include, for example, vectors comprising expression control sequences from SV40, bovine papilloma virus, adenovirus and cytomegalovirus. Useful expression vectors for bacterial hosts include known bacterial plasmids, such as plasmids from Esherichia coli, including pCR1, pBR322, pMB9 and their derivatives, wider host range plasmids, such as M13 and filamentous single-stranded DNA phages. Preferred E. coli vectors include pL vectors containing the lambda phage pL promoter (U.S. Pat. No. 4,874,702), pET vectors containing the T7 polymerase promoter (Studier et al., Methods in Enzymology 185: 60-89, 1990 1) and the pSP72 vector (Kaelin et al., supra). Useful expression vectors for yeast cells, for example, include the 2 T and centromere plasmids.

In addition, any of a wide variety of expression control sequences may be used in these vectors. Such useful expression control sequences include the expression control sequences associated with structural genes of the foregoing expression vectors. Examples of useful expression control sequences include, for example, the early and late promoters of SV40 or adenovirus, the lac system, the trp system, the TAC or TRC system, the major operator and promoter regions of phage lambda, for example pL, the control regions of fd coat protein, the promoter for 3-phosphoglycerate kinase or other glycolytic enzymes, the promoters of acid phosphatase, e.g., Pho5, the promoters of the yeast α-mating system and other sequences known to control the expression of genes of prokaryotic or eukaryotic cells and their viruses, and various combinations thereof.

Any suitable host may be used to produce in quantity the isolated hedgehog polypeptides described herein, including bacteria, fungi (including yeasts), plants, insects, mammals, or other appropriate animal cells or cell lines, as well as transgenic animals or plants. More particularly, these hosts may include well known eukaryotic and prokaryotic hosts, such as strains of E. coli Pseudomonas, Bacillus, Streptomyces, fungi, yeast (e.g., Hansenula ), insect cells such as Spodoptera frugiperda (SF9), and High Five™ (see Example 1), animal cells such as Chinese hamster ovary (CHO), mouse cells such as NS/O cells, African green monkey cells COS1, COS 7, BSC 1, BSC 40, and BMT 10, and human cells, as well as plant cells.

It should be understood that not all vectors and expression control sequences will function equally well to express a given isolated polypeptide. Neither will all hosts function equally well with the same expression system. However, one of skill in the art may make a selection among these vectors, expression control systems and hosts without undue experimentation. For example, to produce isolated polypeptide of interest in large-scale animal culture, the copy number of the expression vector must be controlled. Amplifiable vectors are well known in the art. See, for example, (41) and U.S. Pat. Nos. 4,470,461 and 5,122,464.

Such operative inking of a DNA sequence to an expression control sequence includes the provision of a translation start signal in the correct reading frame upstream of the DNA sequence. If the particular DNA sequence being expressed does not begin with a methionine, the start signal will result in an additional amino acid (methionine) being located at the N-terminus of the product. If a hydrophobic moiety is to be linked to the N-terminal methionyl-containing protein, the protein may be employed directly in the compositions of the invention. Neverthless, since the preferred N-terminal end of the protein is to consist of a cysteine (or functional equivalent) the methionine must be removed before use. Methods are available in the art to remove such N-terminal methionines from polypeptides expressed with them. For example, certain hosts and fermentation conditions permit removal of substantially all of the N-terminal methionine in vivo. Other hosts require in vitro removal of the N-terminal methionine. Such in vitro and in vivo methods are well known in the art.

The proteins produced by a transformed host can be purified according to any suitable method. Such standard methods include chromatography (e.g., ion exchange, affinity, and sizing column chromatography), centrifugation, differential solubility, or by any other standard technique for protein purification. For immunoaffinity chromatography (See Example 1), a protein such as Sonic hedgehog may be isolated by binding it to an affinity column comprising of antibodies that were raised against Sonic hedgehog, or a related protein and were affixed to a stationary support. Alternatively, affinity tags such as hexahistidine, maltose binding domain, influenza coat sequence, and glutathione-S-transferase can be attached to the protein to allow easy purification by passage over an appropriate affinity column. Isolated proteins can also be characterized physically using such techniques as proteolysis, nuclear magnetic resonance, and X-ray crystallography.

A. Production of Fragments and Analogs

Fragments of an isolated protein (e.g., fragments of SEQ ID NOS: 1-4) can also be produced efficiently by recombinant methods, by proteolytic digestion, or by chemical synthesis using methods known to those of skill in the art. In recombinant methods, internal or terminal fragments of a polypeptide can be generated by removing one or more nucleotides from one end (for a terminal fragment) or both ends (for an internal fragment) of a DNA sequence which encodes for the isolated hedgehog polypeptide. Expression of the mutagenized DNA produces polypeptide fragments. Digestion with “end nibbling” endonucleases can also generate DNAs which encode an array of fragments. DNAs which encode fragments of a protein can also be generated by random shearing, restriction digestion, or a combination or both. Protein fragments can be generated directly from intact proteins. Peptides can be cleaved specifically by proteolytic enzymes, including, but not limited to plasmin, thrombin, trypsin, chymotrypsin, or pepsin. Each of these enzymes is specific for the type of peptide bond it attacks. Trypsin catalyzes the hydrolysis of peptide bonds in which the carbonyl group is from a basic amino acid, usually arginine or lysine. Pepsin and chymotrypsin catalyse the hydrolysis of peptide bonds from aromatic amino acids, such as tryptophan, tyrosine, and phenylalanine. Alternative sets of cleaved protein fragments are generated by preventing cleavage at a site which is suceptible to a proteolytic enzyme. For instance, reaction of the ε-amino acid group of lysine with ethyltrifluorothioacetate in mildly basic solution yields blocked amino acid residues whose adjacent peptide bond is no longer susceptible to hydrolysis by trypsin. Proteins can be modified to create peptide linkages that are susceptible to proteolytic enzymes. For instance, alkylation of cysteine residues with β-haloethylamines yields peptide linkages that are hydrolyzed by trypsin (51). In addition, chemical reagents that cleave peptide chains at specific residues can be used. For example, cyanogen bromide cleaves peptides at methionine residues (52). Thus, by treating proteins with various combinations of modifiers, proteolytic enzymes and/or chemical reagents, the proteins may be divided into fragments of a desired length with no overlap of the fragments, or divided into overlapping fragments of a desired length.

Fragments can also be synthesized chemically using techniques known in the art such as the Merrifield solid phase F moc or t-Boc chemistry. Merrifield, Recent Progress in Hormone Research 23: 451 (1967)

Examples of prior art methods which allow production and testing of fragments and analogs are discussed below. These, or analogous methods may be used to make and screen fragments and analogs of an isolated polypeptide (e.g., hedgehog) which can be shown to have biological activity. An exemplary method to test whether fragments and analogs of hedgehog have biological activity is found in Example 3.

B. Production of Altered DNA and Peptide Sequences: Random Methods

Amino acid sequence variants of a protein (such as variants of SEQ ID NOS: 1-4) can be prepared by random mutagenesis of DNA which encodes the protein or a particular portion thereof. Useful methods include PCR mutagenesis and saturation mutagenesis. A library of random amino acid sequence variants can also be generated by the expression of a set of degenerate oligonucleotide sequences. Methods of generating amino acid sequence variants of a given protein using altered DNA and peptides are well-known in the art. The following examples of such methods are not intended to limit the scope of the present invention, but merely serve to illustrate representative techniques. Persons having ordinary skill in the art will recognize that other methods are also useful in this regard.

PCR Mutagenesis:

Briefly, Taq polymerase (or another polymerase) is used to introduce random mutations into a cloned fragment of DNA (42). PCR conditions are chosen so that the fidelity of DNA synthesis is reduced by Taq DNA polymers using, for instance, a dGTP/dATP ratio of five and adding Mn²⁺ to the PCR reaction. The pool of amplified DNA fragments is inserted into appropriate cloning vectors to provide random mutant libraries.

Saturation Mutagenesis:

One method is described generally in (43). Briefly, the technique includes generation of mutations by chemical treatment or irradiation of single stranded DNA in vitro, and synthesis of a cDNA strand. The mutation frequency is modulated by the severity of the treatment and essentially all possible base substitutions can be obtained.

Degenerate Oligonucleotide Mutagenesis:

A library of homologous peptides can be generated from a set of degenerate oligonucleotide sequences. Chemical synthesis of degenerate sequences can by performed in an automatic DNA synthesizer, and the synthetic genes are then ligated into an appropriate expression vector. See for example (44, 45) and Itakura et al., Recombinant DNA, Proc. 3rd Cleveland Symposium on Macromolecules, pp. 273-289 (A. G. Walton, ed.), Elsevier, Amsterdam, 1981.

C. Production of Altered DNA and Peptide Sequences: Directed Methods

Non-random, or directed, mutagenesis provides specific sequences or mutations in specific portions of a polynucleotide sequence that encodes an isolated polypeptide, to provide variants which include deletions, insertions, or substitutions of residues of the known amino acid sequence of the isolated polypeptide. The mutation sites may be modified individually or in series, for instance by: (1) substituting first with conserved amino acids and then with more radical choices depending on the results achieved; (2) deleting the target residue; or (3) inserting residues of the same or a different class adjacent to the located site, or combinations of options 1-3.

Clearly, such site-directed methods are one way in which an N-terminal cysteine (or a functional equivalent) can be introduced into a given polypeptide sequence to provide the attachment site for a hydrophobic moiety.

Alanine scanning Mutagenesis:

This method locates those residues or regions of a desired protein that are preferred locations for mutagenesis (46). In alanine screening, a residue or group of target residues are selected and replaced by alanine. This replacement can affect the interaction of the amino acid with neighboring amino acids and/or with the surrounding aqueous or membrane environment. Those having functional sensitivity to the substitutions are then refined by introducing further or other variants at, or for, the sites of substitution.

Oligonucleotide-Mediated Mutagenesis:

One version of this method may be used to prepare substitution, deletion, and insertion variants of DNA (47). Briefly, the desired DNA is altered by hybridizing an oligonucleotide primer encoding a DNA mutation to a DNA template which typically is the single stranded form of a plasmid or phage containing the unaltered or wild type DNA sequence template of the desired protein (e.g., the Hedgehog protein). After hybridization, a DNA polymerase is used to make the second and complementary strand of DNA of the template that will incorporate the oligonucleotide primer, and will code for the selected alteration in the desired DNA sequence. Generally, oligonucleotides of at least 25 nucleotides in length are used. An optimal oligonucleotide will have 12 to 15 nucleotides that are completely complementary to the template on either side of the mutation. This ensures that the oligonucleotide will hybridize properly to the single-stranded DNA template molecule.

Cassette Mutagenesis:

This method (48) requires a plasmid or other vector that contains the protein subunit DNA to be mutated. The codon(s) in the protein subunit DNA are identified and there is inserted a unique restriction endonuclease site on each side of the identified mutation site(s), using the above-described oligonucleotide-directed mutagenesis method. The plasmid is then cut at these sites to linearize it. A double-stranded oligonucleotide encoding the sequence of the DNA between the restriction sites but containing the desired mutation(s) is synthesized using standard procedures. The two strands are synthesized separately and then hybridized together using standard methods. This double-stranded oligonucleotide is the “cassette” and it has 3′ and 5′ ends that are compatible with the ends of the linearized plasmid so that it can be directly ligated therein. The plasmid now contains the mutated desired protein subunit DNA sequence.

Combinatorial Mutagenesis:

In one version of this method (Ladner et al., WO 88/06630), the amino acid sequences for a group of homologs or other related proteins are aligned, preferably to promote the highest homology possible. All of the amino acids which appear at a given position of the aligned sequences can be selected to create a degenerate set of combinatorial sequences. The variegated library is generated by combinatorial mutagenesis at the nucleic acid level, and is encoded by a variegated gene library. For instance, a mixture of synthetic oligonucleotides can be ligated enzymically into the gene sequence such that the degenerate set of potential sequences are expressible as individual peptides, or alternatively, as a set of proteins containing the entire set of degenerate sequences.

D. Other Variants of Isolated Polypeptides

Included in the invention are isolated molecules that are: allelic variants, natural mutants, induced mutants, and proteins encoded by DNA that hybridizes under high or low stringency conditions to a nucleic acid which encodes a polypeptide such as the N-terminal fragment of Sonic hedgehog (SEQ ID NO: 1) and polypeptides bound specifically by antisera to hedgehog peptides, especially by antisera to an active site or binding site of hedgehog. All variants described herein are expected to: (i) retain the biological function of the original protein and (ii) retain the ability to link to a hydrophobic moiety (e.g, a lipid).

The methods of the invention also feature uses of fragments, preferably biologically active fragments, or analogs of an isolated peptide such as hedgehog. Specifically, a biologically active fragment or analog is one having any in vivo or in vitro activity which is characteristic of the peptide shown in SEQ ID NOS: 1-4 or of other naturally occurring isolated hedgehog. Most preferably, the hydrophobically-modified fragment or analog has at least 10%, preferably 40% or greater, or most preferably at least 90% of the activity of Sonic hedgehog (See Example 3) in any in vivo or in vitro assay.

Analogs can differ from naturally occurring isolated protein in amino acid sequence or in ways that do not involve sequence, or both. The most preferred polypeptides of the invention have preferred non-sequence modifications that include in vivo or in vitro chemical derivatization (e.g., of their N-terminal end), as well as possible changes in acetylation, methylation, phosphorylation, amidation, carboxylation, or glycosylation.

Other analogs include a protein such as Sonic hedgehog or its biologically active fragments whose sequences differ from the wild type consensus sequence (e.g., SEQ ID NO: 4, 15 or 16) by one or more conservative amino acid substitutions or by one or more non conservative amino acid substitutions, or by deletions or insertions which do not abolish the isolated protein's biological activity. Conservative substitutions typically include the substitution of one amino acid for another with similar characteristics such as substitutions within the following groups: valine, alanine and glycine; leucine and isoleucine; aspartic acid and glutamic acid; asparagine and glutamine; serine and threonine; lysine and arginine; and phenylalanine and tyrosine. The non-polar hydrophobic amino acids include alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan, and methionine. The polar neutral amino acids include glycine, serine, threonine, cysteine, tyrosine, asparagine, and glutamine. The positively charged (basic) amino acids include arginine, lysine, and histidine. The negatively charged (acidic) amino acids include aspartic acid and glutamic acid. Other conservative substitutions can be readily known by workers of ordinary skill. For example, for the amino acid alanine, a conservative substitution can be taken from any one of D-alanine, glycine, beta-alanine, L-cysteine, and D-cysteine. For lysine, a replacement can be any one of D-lysine, arginine, D-arginine, homo-arginine, methionine, D-methionine, ornithine, or D-ornithine.

Generally, substitutions that may be expected to induce changes in the functional properties of isolated polypeptides are those in which: (i) a polar residue, e.g., serine or threonine, is substituted for (or by) a hydrophobic residue, e.g., leucine, isoleucine, phenylalanine, or alanine; (ii) a cysteine residue is substituted for (or by) any other residue (See Example 10); (iii) a residue having an electropositive side chain, e.g., lysine, arginine or histidine, is substituted for (or by) a residue having an electronegative side chain, e.g., glutamic acid or aspartic acid; or (iv) a residue having a bulky side chain, e.g., phenylalanine, is substituted for (or by) one not having such a side chain, e.g., glycine.

Other analogs used within the methods of the invention are those with modifications which increase peptide stability. Such analogs may contain, for example, one or more non-peptide bonds (which replace the peptide bonds) in the peptide sequence. Also included are: analogs that include residues other than naturally occurring L-amino acids, such as D-amino acids or non-naturally occurring or synthetic amino acids such as beta or gamma amino acids and cyclic analogs. Incorporation of D- instead of L-amino acids into the isolated hedgehog polypeptide may increase its resistance to proteases. See, U.S. Pat. No. 5,219,990 supra.

The term “fragment”, as applied to an isolated hedgehog analog, can be as small as a single amino acid provided that it retains biological activity. It may be at least about 20 residues, more typically at least about 40 residues, preferably at least about 60 residues in length. Fragments can be generated by methods known to those skilled in the art. The ability of a candidate fragment to exhibit isolated hedgehog biological activity can be also assessed by methods known to those skilled in the art as described herein.

V. Making Hydrophobic Derivatives

The inventors have discovered that increasing the overall hydrophobic nature of a signaling protein, such as a hedgehog protein, increases the biological activity of the protein. The potency of a signaling protein such as hedgehog can be increased by: (a) chemically modifying, such as by adding a hydrophobic moiety to, the sulfhydryl and/or to the α-amine of the N-terninal cysteine (Examples 8 and 9); (b) replacing the N-terminal cysteine with a hydrophobic amino acid (Example 10); or (c) replacing the N-terminal cysteine with a different amino acid and then chemically modifying the substituted residue so as to add a hydrophobic moiety at the site of the substitution.

Additionally, modification of a protein such as hedgehog protein at an internal residue on the surface of the protein with a hydrophobic moiety by: (a) replacing the internal residue with a hydrophobic amino acid; or (b) replacing the internal residue with a different amino acid and then chemically modifying the substituted residue so as to add a hydrophobic moiety at the site of the substitution (See Example 10), will retain or enhance the biological activity of the protein.

Additionally, modification of a protein such as a hedgehog protein at the C-terminus with a hydrophobic moiety by: (a) replacing the C-terminal residue with a hydrophobic amino acid; or (b) replacing the C-terminal residue with a different amino acid and then chemically modifying the substituted residue so as to add a hydrophobic moiety at the site of the substitution, will retain or enhance the biological activity of the protein.

There are a wide range of lipophilic moieties with which hedgehog polypeptides can be derivatived. A lipophilic group can be, for example, a relatively long chain alkyl or cycloalkyl (preferably n-alkyl) group having approximately 7 to 30 carbons. The alkyl group may terminate with a hydroxy or primary amine “tail”. To further illustrate, lipophilic molecules include naturally-occurring and synthetic aromatic and non-aromatic moieties such as fatty acids, esters and alcohols, other lipid molecules, cage structures such as adamantane and buckminsterfullerenes, and aromatic hydrocarbons such as benzene, perylene, phenanthrene, anthracene, naphthalene, pyrene, chrysene, and naphthacene.

Particularly useful as lipophilic molecules are alicyclic hydrocarbons, saturated and unsaturated fatty acids and other lipid and phospholipid moieties, waxes, cholesterol, isoprenoids, terpenes and polyalicyclic hydrocarbons including adamantane and buckminsterfullerenes, vitamins, polyethylene glycol or oligoethylene glycol, (C1-C18)-alkyl phosphate diesters, —O—CH2—CH(OH)—O—(C12—C18)-alkyl, and in particular conjugates with pyrene derivatives. The lipophilic moiety can be a lipophilic dye suitable for use in the invention include, but are not limited to, diphenylhexatriene, Nile Red, N-phenyl-1-naphthylamine, Prodan, Laurodan, Pyrene, Perylene, rhodamine, rhodamine B, tetramethylrhodamine, Texas Red, sulforhodamine, 1,1′-didodecyl-3,3,3′,3′tetramethylindocarbocyanine perchlorate, octadecyl rhodamine B and the BODIPY dyes available from Molecular Probes Inc.

Other exemplary lipophilic moietites include aliphatic carbonyl radical groups include 1- or 2-adamantylacetyl, 3-methyladamant-1-ylacetyl, 3-methyl-3-bromo-1-adamantylacetyl, 1-decalinacetyl, camphoracetyl, camphaneacetyl, noradamantylacetyl, norbornaneacetyl, bicyclo[2.2.2]-oct-5-eneacetyl, 1-methoxybicyclo[2.2.2]-oct-5-ene-2-carbonyl, cis-5-norbornene-endo-2,3-dicarbonyl, 5-norbornen-2-ylacetyl, (1R)-(−)-myrtentaneacetyl, 2-norbornaneacetyl, anti-3-oxo-tricyclo[2.2.1.0<2,6>]-heptane-7-carbonyl, decanoyl, dodecanoyl, dodecenoyl, tetradecadienoyl, decynoyl or dodecynoyl.

Structures of exemplary hydrophobic modifications are shown in FIG. 12. If an appropriate amino acid is not available at a specific position, site-directed mutagenesis can be used to place a reactive amino acid at that site. Reactive amino acids include cysteine, lysine, histidine, aspartic acid, glutamic acid, serine, threonine, tyrosine, arginine, methionine, and tryptophan. Mutagenesis could be used to place the reactive amino acid at the N- or C-terminus or at an internal position.

For example, we have discovered that it is possible to chemically modify an N-terminal cysteine of a biologically active protein, such as a hedgehog protein, or eliminate the N-terminal cysteine altogether and still retain the protein's biological activity, provided that the modified or substituted chemical moiety is hydrophobic. The inventors have found that enhancement of hedgehog's biological activity roughly correlates with the hydrophobicity of the modification. In addition to enhancing the protein's activity, modifying or replacing the N-terminal cysteine eliminates unwanted cross reactions and/or modifications of the cysteine that can occur during production, purification, formulation, and storage of the protein. The thiol of an N-terminal cysteine is very reactive due to its proximity to the α-amine which lowers the pKa of the cysteine and increases proton dissociation and formation of the reactive thiolate ion at neutral or acid pH.

We have demonstrated that replacement of the N-terminal cysteine of hedgehog with a hydrophobic amino acid results in a protein with increased potency in a cell-based signaling assay. By replacing the cysteine, this approach eliminates the problem of suppressing other unwanted modifications of the cysteine that can occur during the production, purification, formulation, and storage of the protein. The generality of this approach is supported by our finding that three different hydrophobic amino acids, phenylalanine, isoleucine, and methionine, each give a more active form of hedgehog. Therefore, replacement of the cysteine with any other hydrophobic amino acid should result in an active protein. Furthermore, since we have found a correlation between the hydrophobicity of an amino acid or chemical modification and the potency of the corresponding modified protein in the C3H10T1/2 assay (e.g. Phe>Met, long chain length fatty acids>short chain length), it could be envisioned that adding more than one hydrophobic amino acid to the hedgehog sequence would increase the potency of the protein beyond that achieved with a single amino acid addition. Indeed, addition of two consecutive isoleucine residues to the N-terminus of human Sonic hedgehog results in an increase in potency in the C3H10T1/2 assay as compared to the mutant with only a single isoleucine added (See Example 10). Thus, adding hydrophobic amino acids at the N- or C-terminus of a hedgehog protein, in a surface loop, or some combination of positions would be expected to give a more active form of the protein. The substituted amino acid need not be one of the 20 common amino acids. Methods have been reported for substituting unnatural amino acids at specific sites in proteins (78, 79) and this would be advantageous if the amino acid was more hydrophobic in character, resistant to proteolytic attack, or could be used to further direct the hedgehog protein to a particular site in vivo that would make its activity more potent or specific. Unnatural amino acids can be incorporated at specific sites in proteins during in vitro translation, and progress is being reported in creating in vivo systems that will allow larger scale production of such modified proteins.

It is unexpected that a protein, such as an hedgehog protein, modified according to the invention, would retain its biological activity. First, the N-terminal cysteine is conserved in all known hedgehog protein sequences including fish, frog, insect, bird, and mammals. Therefore, it is reasonable to expect that the free sulfhydryl of the N-terminal cysteine is important to the protein's structure or activity. Second, hedgehog proteins lacking an N-terminal cysteine, due to proteolytic cleavage or mutation to hydrophilic amino acids (e.g., aspartic acid or histidine) are inactive in a the cell-based C3H10T1/2 assay, such as that described in Example 3.

There are many modifications of the N-terminal cysteine which protect the thiol with and append a hydrophobic moiety. These modifications are discussed in more detail below. One of skill in the art is capable of determining which modification is most appropriate for a particular therapeutic use. Factors affecting such a determination include cost and ease of production, purification and formulation, solubility, stability, potency, pharmacodynamics and kinetics, safety, immunogenicity, and tissue targeting.

A. Chemical Modifications of Primary Amino Acid Sequence

The chemical modification of the N-terminal cysteine to protect the thiol, with concomitant activation by a hydrophobic moiety, can be carried out in numerous ways by someone skilled in the art. The sulfhydryl moiety, with the thiolate ion as the active species, is the most reactive functional group in a protein. There are many reagents that react faster with the thiol than any other groups. See Chemistry of Protein Conjugation and Cross-Linking (S. S. Wong, CRC Press, Boca Raton, Fla., 1991). The thiol of an N-terminal cysteine, such as found in all hedgehog proteins, would be expected to be more reactive than internal cysteines within the sequence. This is because the close proximity to the α-amine will lower the pKa of the thiol resulting in a greater degree of proton dissociation to the reactive thiolate ion at neutral or acid pH. In addition, the cysteine at the N-terminus of the structure is more likely to be exposed than the other two cysteines in the hedgehog sequence that are found buried in the protein structure. We have shown that the N-terminal cysteine is the only amino acid modified after a 1 h reaction with N-ethylmaleimide at pH 5.5 (See Example 9), and after a 18 h reaction with N-isopropyliodoacetamide at pH 7.0 (See Example 9). Other examples of such methods would be reaction with other α-haloacetyl compounds, organomercurials, disulfide reagents, and other N-substituted maleimides. Numerous hydrophobic derivatives of these active species are available commercially (e.g., ethyl iodoacetate (Aldrich, Milwaukee Wis.), phenyl disulfide (Aldrich), and N-pyrenemaleimide (Molecular Probes, Eugene Oreg.)) or could be synthesized readily (e.g., N-alkyliodoacetamides (84), N-alkylmaleimides (85), and organomercurials (86). We ave shown that the N-terminal cysteine of human Sonic hedgehog can be specifically odified with N-isopropyliodoacetamide and that the hydrophobically-modified protein is 2-fold more potent in the C3H10T1/2 assay than the unmodified protein (See Example 9). It is expected that modification of Shh with a long-chain alkyl iodoacetamide derivative will result in a modified protein with even greater enhancement of potency. Such N-alkyliodoacetamides can be synthesized readily by ones skilled in the art, using commercially available starting materials.

Another aspect to the reactivity of an N-terminal cysteine is that it can take part in reaction chemistries unique to its 1,2-aminothiol configuration. One example is the reaction with thioester groups to form an N-terminal amide group via a rapid S to N shift of the thioester. This reaction chemistry can couple together synthetic peptides and can be used to add single or multiple, natural or unnatural, amino acids or other hydrophobic groups via the appropriately activated peptide. Another example, demonstrated herein, is the reaction with aldehydes to form the thiazolidine adduct. Numerous hydrophobic derivatives of thiol esters (e.g., C2-C24 saturated and unsaturated fatty acyl Coenzyme A esters (Sigma Chemical Co., St. Louis Mo.)), aldehydes (e.g., butyraldehyde, n-decyl aldehyde, and n-myristyl aldehyde (Aldrich)), and ketones (e.g., 2-, 3-, and 4-decanone (Aldrich)) are available commercially or could be synthesized readily (87, 88). In a similar manner, thiomorpholine derivatives exemplified by the 1-bromo-2-butanone chemistry described in Example 9 could be prepared from a variety of α-haloketone starting materials (88). Because of the ease of finding alternative routes to modifying the thiol of the N-terminal cysteine, or any cysteine in a protein, we do not wish to be bound by the specific examples demonstrated here.

The α-amine of a protein can be modified preferentially relative to other amines in a protein because its lower pKa results in higher amounts of the reactive unprotonated form at neutral or acidic pH. We have shown that modification of the N-terminal amine with a long chain fatty amide group, while maintaining a free cysteine thiol group, activates the hedgehog protein by as much as two orders of magnitude (See Example 8). Therefore chemistries that can be directed to react preferentially with the N-terminal amine would be expected to be of use in increasing the potency of the hedgehog proteins. Aryl halides, aldehydes and ketones, acid anhydrides, isocyanates, isothiocyanates, imidoesters, acid halides, N-hydroxysuccinimidyl (e.g., sulfo-NHS-acetate), nitrophenyl esters, acylimidazoles, and other activated esters are among those known to react with amine functions.

Active thioesters include acylated derivatives of thiols, wherein the thiol has a molecular weight less than 500 amu and a pKa lower than that of ethanethiol, preferably aromatic or heteroaromatic thiols, even more preferably acylated thiophenols bearing one, or preferably two or more electron withdrawing groups. Suitable electron-withdrawing substituents include nitro, carbonyl (e.g., ester, aldehyde, ketone, amide, carboxyl, or thioester groups), cyano, halogen (preferably chloro or fluoro), sulfonyl (e.g., sulfonamide, sulfonate, sulfonic acid, or sulfone groups), or phosphonyl (e.g., phosphate, phosphate, etc.) groups, preferably nitro, carbonyl, cyano, or halogen groups. In certain embodiments, the active thioesters comprise derivatives of fatty acids having from 2 to 24 carbon atoms. In certain other embodiments, the active thioesters are derivatives of natural or unnatural amino acids, preferably tripeptides or smaller. In further embodiments, the active thioesters include compounds having two or more active thioester moieties, in order to link two or more polypeptides together.

For example, in one embodiment of the present invention, the active thioester is a compound represented by general formula (I):

wherein R represents an organic substituent having a molecular weight less than 1000 amu, preferably less than 500 amu, more preferably less than 250 amu, and A represents an organic substituent selected such that HSR has a pKa lower than that of ethanethiol. For example, A may represent 2,2,2-trifluoroethyl, a substituted or unsubstituted aryl ring, etc. In certain embodiments, A is a heteroaryl group, such as pyridyl. In certain embodiments, R represents a carbon chain having from 1 to 23 carbon atoms. In certain other embodiments, R represents from 1 to 20 natural or unnatural amino acids, preferably three or fewer.

In certain preferred embodiments, the structure of the active thioester may be represented by general formula (II):

wherein R is an organic substituent having a molecular weight less than 1000 amu, preferably less than 500 amu, more preferably less than 250 amu, and V, W, X, Y, and Z represent, independently, H or any substituent having a molecular weight less than 200 amu, preferably less than 100 amu. In preferred embodiments, V, W, X, Y, and Z represent, independently, H, halogen, lower alkyl, lower alkenyl, carbonyl group (e.g. ester, carboxyl, ketone, amido, or aldehyde), thiocarbonyl (e.g. thiolester, thiolcarboxylate, or thiolformate), amino, acylamino, amidino, cyano, nitro, azido, sulfonyl, sulfoxido, sulfate, sulfonate, sulfamoyl, sulfonamido, phosphoryl, phosphonate, phosphinate, —(CH₂)_(m)—R₈, —(CH₂)_(m)—OH, —(CH₂)_(m)—O-lower alkyl, —(CH₂)_(m)—O-lower alkenyl, —O—(CH₂)_(n)—R₈, —(CH₂)_(m)—SH, —(CH₂)_(m)—S-lower alkyl, —(CH₂)_(m)—S-lower alkenyl, —S—(CH₂)_(n)—R₈, —(CH₂)_(m)—NH₂, —(CH₂)_(m)—NH-lower alkyl, —(CH₂)_(m)—NH-lower alkenyl, —NH—(CH₂)_(n)—R₈, or protected forms of the above, or a solid or polymeric support. In more preferred embodiments, at least one of V, W, X, Y, and Z represents an electron withdrawing group, such as halogen (preferably fluoro or chloro), carbonyl group, cyano, nitro, sulfonyl, sulfate, sulfonate, sulfamoyl, phosphoryl, phosphate, phosphinate, or protected forms of the above, even more preferably halogen (preferably fluoro or chloro), carbonyl group, cyano, or nitro. In further preferred embodiments, two or more of V, W, X, Y, and Z are electron withdrawing groups. In certain embodiments, two adjacent groups of V, W, X, Y, and Z may together form an aliphatic, aromatic, or heterocylic ring. In a preferred embodiment, W represents CO₂H and X represents NO₂. In certain embodiments, R represents a carbon chain having from 1 to 23 carbon atoms. In certain other embodiments, R represents from 1 to 20 natural or unnatural amino acids, preferably three or fewer.

When selecting an active thioester for modifying a protein, it is important to select a thioester having suitable reactivity. For example, active thioesters according to general formula (II), wherein only one of V, W, X, Y, and Z represents an electron-withdrawing group will generally be less reactive than those wherein two or more of V, W, X, Y, and Z represent electron-withdrawing groups, depending on the electron-withdrawing capability of the particular electron-withdrawing groups present. More reactive thioesters may modify more sites of a protein or polypeptide, or may require shorter reaction times, or may modify the protein or polypeptide under midler conditions than less reactive thioesters.

By replacing the N-terminal cysteine of hedgehog with certain other amino acids, other chemical methods can be used to add a hydrophobic moiety to the N-terminus. One example is to place a serine or threonine at the N-terminus, oxidize this amino acid to form an aldehyde, and then conjugate the protein with a chemical moiety containing a 1,2-aminothiol structure (e.g., a cysteine). A second example would be to place a histidine at the N-terminus to couple to a C-terminal thiocarboxylic acid.

Chemical Modification of Other Amino Acids.

There are specific chemical methods for the modification of many other amino acids. Therefore another route for synthesizing a more active-form of hedgehog would be to chemically attach a hydrophobic moiety to an amino acid in hedgehog other than to the N-terminal cysteine. If an appropriate amino acid is not available at the desired position, site-directed mutagenesis could be used to place the reactive amino acid at that site in the hedgehog structure, whether at the N- or C-terminus or at another position. Reactive amino acids would include cysteine, lysine, histidine, aspartic acid, glutamic acid, serine, threonine, tyrosine, arginine, methionine, and tryptophan. Thus the goal of creating a more hydrophobic form of hedgehog could be attained by many chemical means and we do not wish to be restricted by a particular chemistry or site of modification since our results support the generality of this approach.

The hedgehog polypeptide can be linked to the hydrophobic moiety in a number of ways including by chemical coupling means, or by genetic engineering.

To illustrate, there are a large number of chemical cross-linking agents that are known to those skilled in the art. For the present invention, the preferred cross-linking agents are heterobifunctional cross-linkers, which can be used to link the hedgehog polypeptide and hydrophobic moiety in a stepwise manner. Heterobifunctional cross-linkers provide the ability to design more specific coupling methods for conjugating to proteins, thereby reducing the occurrences of unwanted side reactions such as homo-protein polymers. A wide variety of heterobifunctional cross-linkers are known in the art. These include: succinimidyl 4-(N-maleimidomethyl) cyclohexane-1-carboxylate (SMCC), m-Maleimidobenzoyl-N-hydroxysuccinimide ester (MBS); N-succinimidyl (4-iodoacetyl) aminobenzoate (SIAB), succinimidyl 4-(p-maleimidophenyl) butyrate (SMPB), 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC); 4-succinimidyloxycarbonyl-a-methyl-a-(2-pyridyldithio)-tolune (SMPT), N-succinimidyl 3-(2-pyridyldithio) propionate (SPDP), succinimidyl 6-[3-(2-pyridyldithio) propionate] hexanoate (LC-SPDP). Those cross-linking agents having N-hydroxysuccinimide moieties can be obtained as the N-hydroxysulfosuccinimide analogs, which generally have greater water solubility. In addition, those cross-linking agents having disulfide bridges within the linking chain can be synthesized instead as the alkyl derivatives so as to reduce the amount of linker cleavage in vivo.

In addition to the heterobifunctional cross-linkers, there exists a number of other cross-linking agents including homobifunctional and photoreactive cross-linkers. Disuccinimidyl suberate (DSS), bismaleimidohexane (BMH) and dimethylpimelimidate.2 HCl (DMP) are examples of useful homobifunctional cross-linking agents, and bis-[β-(4-azidosalicylamido)ethyl]disulfide (BASED) and N-succinimidyl-6(4′-azido-2′-nitrophenyl-amino)hexanoate (SANPAH) are examples of useful photoreactive cross-linkers for use in this invention. For a recent review of protein coupling techniques, see Means et al. (1990) Bioconjugate Chemistry 1:2-12, incorporated by reference herein.

One particularly usefll class of heterobifunctional cross-linkers, included above, contain the primary amine reactive group, N-hydroxysuccinimide (NHS), or its water soluble analog N-hydroxysulfosuccinimide (sulfo-NHS). Primary amines (lysine epsilon groups) at alkaline pH's are unprotonated and react by nucleophilic attack on NHS or sulfo-NHS esters. This reaction results in the formation of an amide bond, and release of NHS or sulfo-NHS as a by-product.

Another reactive group useful as part of a heterobifunctional cross-linker is a thiol reactive group. Common thiol reactive groups include maleimides, halogens, and pyridyl disulfides. Maleimides react specifically with free sulfhydryls (cysteine residues) in minutes, under slightly acidic to neutral (pH 6.5-7.5) conditions. Halogens (iodoacetyl functions) react with —SH groups at physiological pH's. Both of these reactive groups result in the formation of stable thioether bonds.

The third component of the heterobifimctional cross-linker is the spacer arm or bridge. The bridge is the structure that connects the two reactive ends. The most apparent attribute of the bridge is its effect on steric hindrance. In some instances, a longer bridge can more easily span the distance necessary to link two complex biomolecules. For instance, SMPB has a span of 14.5 angstroms.

Preparing protein-protein conjugates using heterobifunctional reagents is a two-step process involving the amine reaction and the sulfhydryl reaction. For the first step, the amine reaction, the protein chosen should contain a primary amine. This can be lysine epsilon amines or a primary alpha amine found at the N-terminus of most proteins. The protein should not contain free sulfhydryl groups. In cases where both proteins to be conjugated contain free sulfhydryl groups, one protein can be modified so that all sulfhydryls are blocked using for instance, N-ethylmaleimide (see Partis et al. (1983) J. Pro. Chem. 2:263, incorporated by reference herein). Ellman's Reagent can be used to calculate the quantity of sulfhydryls in a particular protein (see for example Ellman et al. (1958) Arch. Biochem. Biophys. 74:443 and Riddles et al. (1979) Anal. Biochem. 94:75, incorporated by reference herein).

The reaction buffer should be free of extraneous amines and sulfhydryls. The pH of the reaction buffer should be 7.0-7.5. This pH range prevents maleimide groups from reacting with amines, preserving the maleimide group for the second reaction with sulfhydryls.

The NHS-ester containing cross-linkers have limited water solubility. They should be dissolved in a minimal amount of organic solvent (DMF or DMSO) before introducing the cross-linker into the reaction mixture. The cross-linker/solvent forms an emulsion which will allow the reaction to occur.

The sulfo-NHS ester analogs are more water soluble, and can be added directly to the reaction buffer. Buffers of high ionic strength should be avoided, as they have a tendency to “salt out” the sulfo-NHS esters. To avoid loss of reactivity due to hydrolysis, the cross-linker is added to the reaction mixture immediately after dissolving the protein solution.

The reactions can be more efficient in concentrated protein solutions. The more alkaline the pH of the reaction mixture, the faster the rate of reaction. The rate of hydrolysis of the NHS and sulfo-NHS esters will also increase with increasing pH. Higher temperatures will increase the reaction rates for both hydrolysis and acylation.

Once the reaction is completed, the first protein is now activated, with a sulfhydryl reactive moiety. The activated protein may be isolated from the reaction mixture by simple gel filtration or dialysis. To carry out the second step of the cross-linking, the sulfhydryl reaction, the lipophilic group chosen for reaction with maleimides, activated halogens, or pyridyl disulfides must contain a free sulfhydryl. Alternatively, a primary amine may be modified with to add a sulfhydryl

In all cases, the buffer should be degassed to prevent oxidation of sulfhydryl groups. EDTA may be added to chelate any oxidizing metals that may be present in the buffer. Buffers should be free of any sulfhydryl containing compounds.

Maleimides react specifically with —SH groups at slightly acidic to neutral pH ranges (6.5-7.5). A neutral pH is sufficient for reactions involving halogens and pyridyl disulfides. Under these conditions, maleimides generally react with —SH groups within a matter of minutes. Longer reaction times are required for halogens and pyridyl disulfides.

The first sulfhydryl reactive-protein prepared in the amine reaction step is mixed with the sulfhydryl-containing lipophilic group under the appropriate buffer conditions. The conjugates can be isolated from the reaction mixture by methods such as gel filtration or by dialysis.

Exemplary activated lipophilic moieties for conjugation include: N-(1-pyrene)maleimide; 2,5-dimethoxystilbene-4′-maleimide, eosin-5-maleimide; fluorescein-5-maleimide; N-(4-(6-dimethylamino-2-benzofuranyl)phenyl)maleimide; benzophenone-4-maleimide; 4-dimethylaminophenylazophenyl-4′-maleimide (DABMI), tetramethylrhodamine-5-maleimide, tetramethylrhodamine-6-maleimide, Rhodamine RedTM C2 maleimide, N-(5-aminopentyl)maleimide, trifluoroacetic acid salt, N-(2-aminoethyl)maleimide, trifluoroacetic acid salt, Oregon GreenTM 488 maleimide, N-(2-((2-(((4-azido-2,3,5,6-tetrafluoro)benzoyl)amino)ethyl)dithio)ethyl)maleimide (TFPAM-SS1), 2-(1-(3-dimethylaminopropyl)-indol-3-yl)-3-(indol-3-yl) maleimide (bisindolylmaleimide; GF 109203X), BODIPY® FL N-(2-aminoethyl)maleimide, N-(7-dimethylamino-4-methylcoumarin-3-yl)maleimide (DACM), AlexaTM 488 C5 maleimide, AlexaTM 594 C5 maleimide, sodium saltN-(1-pyrene)maleimide, 2,5-dimethoxystilbene-4′-maleimide, eosin-5-maleimide, fluorescein-5-maleimide, N-(4-(6-dimethylamino-2-benzofuranyl)phenyl)maleimide, benzophenone-4-maleimide, 4-dimethylaminophenylazophenyl-4′-maleimide, 1-(2-maleimidylethyl)-4-(5-(4-methoxyphenyl)oxazol-2-yl)pyridinium methanesulfonate, tetramethylrhodamine-5-maleimide, tetramethylrhodamine-6-maleimide, Rhodamine RedTM C2 maleimide, N-(5-aminopentyl)maleimide, N-(2-aminoethyl)maleimide, N-(2-((2-(((4-azido-2,3,5,6-tetrafluoro)benzoyl)amino)ethyl)dithio)ethyl)maleimide, 2-(1-(3-dimethylaminopropyl)-indol-3-yl)-3-(indol-3-yl) maleimide, N-(7-dimethylamino-4-methylcoumarin-3-yl)maleimide (DACM), 11H-Benzo[a]fluorene, Benzo[a]pyrene.

In one embodiment, the hedgehog polypeptide can be derivatived using pyrene maleimide, which can be purchased from Molecular Probes (Eugene, Oreg.), e.g., N-(1-pyrene)maleimide or 1-pyrenemethyl iodoacetate (PMIA ester). As illustrated in FIG. 1, the pyrene-derived hedgehog protein had an activity profile indicating that it was nearly 2 orders of magnitude more active than the unmodified form of the protein.

B. Making Hydrophobic Peptide Derivatives

According to the invention, the protein can also be modified using a hydrophobic peptide. As used herein, the term “peptide” includes a sequence of at least one amino acid residue. Preferably, the peptide has a length between one amino acid and 18-26 amino acids, the latter being the typical length of a membrane spanning segment of a protein. To create a peptide with hydrophobic character, the amino acids are selected predominantly from the following hydrophobic amino acids:

phenylalanine, isoleucine, leucine, valine, methionine, tryptophan, alanine, proline, and tyrosine. The hydrophobic peptide can also contain unnatural amino acid analogs with hydrophobic character or D-amino acids, peptoid bonds, N-terminal acetylation or other features that decrease the peptide's susceptibility to proteolysis. Methods for substituting unnatural amino acids at specific sites in proteins are known (78, 79).

Generally, a hydrophobic peptide is appended to various sites on a protein. One site can be the N-terminal residue. Alternatively, the hydrophobic peptide is substituted in place of the N-terminal residue. In another embodiment, a hydrophobic peptide is appended to the C-terminus of the protein. Alternatively, the hydrophobic peptide is substituted in place of the C-terminal residue. The C-terminus can be the native C-terminal amino acid but it may also be the C-terminus of a truncated protein so that the hydrophobic peptide is appended to the final C-terminal amino acid of the truncated form, which is still referred to as the “C-terminus”. A truncated hedgehog protein will retain activity when up to eleven amino acids are deleted from the native C-terminal sequence. The hydrophobic peptide may also be inserted between the N-terminal residue and the internal residue immediately adjacent to the N-terminal residue, or between the C-terminal residue and the residue immediately adjacent to the C-terminal residue, or between two internal residues.

In certain embodiments, the lipophilic moiety is an amphipathic polypeptide, such as magainin, cecropin, attacin, melittin, gramicidin S, alpha-toxin of Staph. aureus, alamethicin or a synthetic amphipathic polypeptide. Fusogenic coat proteins from viral particles can also be a convenient source of amphipathic sequences for the subject hedgehog proteins

C. Making Lipid Derivatives

Another form of protein encompassed by the invention is a protein derivatized with a variety of lipid moieties. Generally, a “lipid” is a member of a heterogenous class of hydrophobic substances characterized by a variable solubility in organic solvents and insolubility, for the most part, in water. The principal classes of lipids that are encompassed within this invention are fatty acids and sterols (e.g., cholesterol). Derivatized proteins of the invention contain fatty acids which are cyclic, acyclic (i.e., straight chain), saturated or unsaturated, mono-carboxylic acids. Exemplary saturated fatty acids have the generic formula: CH₃ (CH₂)n COOH. The following table lists examples of some fatty acids that can be derivatized conveniently using conventional chemical methods.

TABLE 2 Exemplary Saturated and Unsaturated Fatty Acids Common Name Saturated Acids: CH₃(CH₂)n COOH Value of n  2 butyric acid  4 caproic acid  6 caprylic acid  8 capric acid 10 lauric acid 12 myristic acid* 14 palmitic acid* 16 stearic acid* 18 arachidic acid* 20 behenic acid 22 lignoceric acid Unsaturated Acids CH₃CH═CHCOOH crotonic acid CH₃(CH₂)₃CH═CH(CH₂)7COOH myristoleic acid* CH₃(CH₂)₅CH═CH (CH₂)₇COOH palmitoleic acid* CH₃(CH₂)₇CH═CH(CH₂)₇COOH oleic acid* CH₃(CH₂)₃(CH₂CH═CH)₂(CH₂)₇COOH linoleic acid CH₃(CH₂CH═CH)₃(CH₂)₇COOH linolenic acid CH₃(CH₂)₃(CH₂CH═CH)₄(CH₂)₃COOH arachidonic acid The asterisk (*) denotes the fatty acids that we found in recombinant hedgehog protein secreted from a soluble construct.

Other lipids that can be attached to the protein include branched-chain fatty acids and those of the phospholipid group such as the phosphatidylinositols (i.e., phosphatidylinositol 4-monophosphate and phosphatidylinositol 4,5-biphosphate), phosphatidycholine, phosphatidylethanolamine, phosphatidylserine, and isoprenoids such as farnesyl or geranyl groups.

We have demonstrated that lipid-modified hedgehog proteins can be purified from either a natural source, or can be obtained by chemically modifying the soluble, unmodified protein. For protein purified from a natural source, we showed that when full-length human Sonic hedgehog (Shh) was expressed in insect cells and membrane-bound Shh purified from the detergent-treated cells using a combination of SP-Sepharose chromatography and immunoaffinity chromatography, that the purified protein migrated on reducing SDS-PAGE gels as a single sharp band with an apparent mass of 20 kDa (See Example 1). The soluble and membrane-bound Shh proteins were readily distinguishable by reverse phase HPLC, where the tethered forms eluted later in the acetonitrile gradient (See Example 1 and FIG. 3). We then demonstrated that human Sonic hedgehog is tethered to cell membranes in two forms, one form that contains a cholesterol, and therefore is analogous to the data reported previously for Drosophila hedgehog (18), and a second novel form that contains both a cholesterol and a palmitic acid modification. Soluble and tethered forms of Shh were analyzed by electrospray mass spectrometry using a triple quadrupole mass spectrometer, equipped with an electrospray ion source (Example 1) as well as by liquid chromatography-mass spectrometry (See Example 1). The identity of the N-terminal peptide from endoproteinase Lys-C digested tethered Shh was confirmed by MALDI PSD mass spectrometric measurement on a MALDI time of flight mass spectrometer. The site of palmitoylation was identified through a combination of peptide mapping and sequence analysis and is at the N-terminus of the protein (residue 1 of the sequence of the mature protein in SEQ ID NOS: 1-4). Both tethered forms were equally as active in the C3H10T1/2 alkaline phosphatase assay, but interestingly both were about 30-times more potent than soluble human Shh lacking the tether(s). The lipid modifications did not significantly affect the apparent binding affinity of Shh for its receptor, patched (FIG. 7).

We next tested the utility of the derivatized forms by assaying the relative potencies of soluble and tethered Shh alone or in the presence of the anti-hedgehog neutralizing Mab 5E1 on C3H10T1/2 cells measuring alkaline phosphatase induction. Moreover, the relative potency of soluble and tethered Shh for binding to patched was assessed on patched-transfected EBNA-293 cells by FACS analysis (Example 3).

For lipid-modified hedgehog obtained by chemically modifying the soluble, unmodified protein, we have showed that palmitic acid and other lipids can be added to soluble Shh to create a lipid-modified forms with increased potency in the C3H10T1/2 assay (Example 8). We have shown (Examples 1, 2, and 8) that the thiol and α-amine on the N-terminal cysteine contribute to the lipid derivatization reaction. Without wishing to be bound by any particular theory, lipid modification on proteins starts with the formation of a thioester intermediate and the lipid moiety is then transferred to the α-amine of the N-terminus through the formation of a cyclic intermediate. Generally, therefore, the reactive lipid moiety can be in the form of thioesters of saturated or unsaturated carboxylic acids such as a Coenzyme A thioesters. Such materials and their derivatives may include, for example, commercially available Coenzyme A derivatives such as palmitoleoyl Coenzyme A, arachidoyl Coenzyme A, arachidonoyl Coenzyme A, lauroyl Coenzyme A and the like. These materials are readily available from Sigma Chemical Company (St. Louis, Mo., 1998 catalog pp. 303-306).

The effect of different lipid moieties on functional activity of hedgehog protein has been assayed (See Example 8 and FIGS. 10 and 11). Similarly, the effect of different lipid moieties on functional activity of other proteins such as those described above in Section III, may be conveniently tested using methods known to workers of ordinary skill. For instance, functional testing of gelsolin (50), various interferons (interferon-α, interferon-β and interferon-γ), the various interleukins (e.g., IL-1, -2, -3, -4, and the like), the tumor necrosis factors-α and -γ, and other growth factors that are lipid-modified according to the invention can be accomplished using well known methods.

Although we have established chemical means by which a fatty acid can be attached to the N-terminal cysteine of hedgehog proteins, it might be expected that lipids can be attached to the same or other sites using enzymically catalyzed reactions. Palmitoylation of proteins in vivo is catalyzed by a class of enzymes known as palmitoyl-CoA:protein S-palmitoyltransferases. Using purified enzymes, in vitro acylation of protein substrates has been demonstrated (80, 81). The substrate specificities of the palmitoyltransferase enzymes are not well defined; an analysis of palmitoylation sites of cellular and viral proteins finds little in the way of a consensus sequence surrounding the modified cysteine residue, but suggests a common presence of a lysine or arginine residue within two amino acids of the cysteine, and large, hydrophobic amino acids near the cysteine. The amino-terminal sequence of Shh, CGPGRGFG, may fit this consensus sequence and serve as a recognition site for palmitoylation.

As an alternative, myristoylation of the amino terminus of hedgehog proteins could be carried out using an N-myristoyl transferase (NMT), a number of which have been well characterized in both mammals (82) and in yeast (83). A recognition site for N-myristoyltransferase could be engineered into the hedgehog N-terminal sequence to facilitate recognition by the enzyme. Both of these strategies would require the use of fatty acyl-coenzyme A derivatives as substrates, as are used for the non-enzymic fatty acylation of human Sonic hedgehog described in Example 8. Alternatively, a protein with an engineered recognition sequence may be myristoylated during expression in a suitable cell line. Another method of modifying a protein such as hedgehog with a hydrophobic moiety is to create a recognition site for the addition of an isoprenoid group at the C-terminus of the protein. The recognition site for farnesyl and geranyl-geranyl addition are known and the protein may be modified during expression in a eukaryotic cell (Gelb et al., Cur. Opin. Chem. Biol. 2: 40-48 (1998)).

VI. Multimeric Protein Complexes

Hydrophobically-modified proteins described herein are particularly amenable to being made into multimeric protein complexes. Multimeric protein complexes of the invention include proteins, optionally attached via their hydrophobic (e.g., lipid) moiety to a vesicle. The vesicle may be a naturally occurring biological membrane, purified away from natural material, or the vesicle may be a synthetic construction. Preferred vesicles are substantially spherical structures made of amphiphiles, e.g., surfactants or phospholipids. The lipids of these spherical vesicles are generally organized in the form of lipids having one or more structural layers, e.g., multilamellar vesicles (multiple onion-like shells of lipid bilayers which encompass an aqueous volume between the bilayers) or micelles.

In particular, liposomes are small, spherical vesicles composed primarily of various types of lipids, phospholipids, and secondary lipophilic components. These components are normally arranged in a bilayer formation, similar to the lipid arrangement of biological membranes.

Typically, the polar end of a component lipid or lipid-like molecule is in contact with the surrounding solution, usually an aqueous solution, while the non-polar, hydrophobic end of the lipid or lipid-like molecule is in contact with the non-polar, hydrophobic end of another lipid or lipid-like molecule. The resulting bilayer membrane (i.e., vesicle) is selectively permeable to molecules of a certain size, hydrophobicity, shape, and net charge. Most vesicles are lipid or lipid-like in nature, although alternative liposome bilayer formulations, comprising a surfactant with either a lipid or a cholesterol, exist.

Liposome vesicles may be particularly preferred in that they find many therapeutic, diagnostic, industrial, and commercial applications. They are used to deliver molecules which are not readily soluble in water, or when directed timed release is desired. Because of their selective permeability to many chemical compounds, liposomes are useful as delivery vehicles for drugs and biological materials. Thus, lipid-derivatized proteins such as hedgehog can be made multimeric by being incorporated into the lipid bilayer of liposome vesicles. Upon reaching the target site, the liposomes may be degraded (for example, by enzymes in the gastro-intestinal tract) or they may fuse with the membranes of cells.

Several methods of preparing vesicles such as liposomes are known. The production of phospholipid vesicles is well known (53). For a general review of commonly used methods, see (54). Among the more common of these are (1) sonication of a solution containing lipids sometimes followed by evaporation/lyophilization and rehydration (see, e.g. Stryer, Biochemistry, pp. 290-291, Freeman & Co., New York, (1988), and (55); (2) homogenization of a lipid solution, sometimes at high pressure or high shearing force (see e.g. U.S. Pat. No. 4,743,449 issued May 10, 1988, and U.S. Pat. No. 4,753,788, issued Jun. 28, 1988), (3) hydration and sometimes sonication of a dried film of vesicle-forming lipids wherein the lipid film is prepared by evaporation of a solution of lipids dissolved in an organic solvent (see e.g. U.S. Pat. No. 4,452,747 issued Jun. 15, 984, U.S. Pat. No. 4,895,719 issued Jan. 23, 1990, and U.S. Pat. No. 4,946,787 issued Aug. 7, 1990), (4) lyophilization or evaporation and rehydration (see e.g. U.S. Pat. No. 4,897,355 issued Jan. 30, 1990, EP 267,050 published Nov. 5, 1988, U.S. Pat. No. 4,776,991 issued Oct. 11, 1988, EP 172,007 published Feb. 19, 1986, and Australian patent application AU-A-48713/85 published Apr. 24, 1986), (5) solvent injection or infusion of a lipid solution into an aqueous medium or vice versa (see e.g. (56); U.S. Pat. No. 4,921,757 issued May 1, 1990, U.S. Pat. No. 4,781,871 issued Nov. 1, 1988, WO 87/02396 published Mar. 24, 1988, and U.S. Pat. No. 4,895,452 issued Jan. 23, 1990), (6) spray drying (see e.g. Australian patent application AU-A-48713/85 published Apr. 24, 1986, and U.S. Pat. No. 4,830,858 issued May 16, 1989), (7) filtration (see e.g. WO 85/01161), (8) reverse-phase evaporation. See e.g. (57); and (9) combinations of the above methods. See e.g. (58) and (59).

Preferred lipids and lipid-like components suitable for use in preparing vesicles include phospholipids, a mixture of phospholipids, polar lipids, neutral lipids, fatty acids, and their derivatives. A preferred lipid has the characteristic that when dispersed alone in water, at a temperature above the lipid transition temperature, they are in a lipid emulsion phase. In certain embodiments, the lipid is a single-aliphatic chain of greater than about 12 carbons and can be either saturated or unsaturated, or substituted in other ways. Suitable lipids include the ester, alcohol, and acid forms of the following fatty acids: stearate, oleic acid, linoleic acid, arachidate, arachidonic acid, and other single-aliphatic chains acids. Further candidates include the ester, alcohol, and acid forms of the retinols, in particular, retinol and retinoic acid. Other preferred lipids include phosphatidylcholine (PC), phosphatidylglycerol (PG) and their derivatives, created synthetically or derived from a variety of natural sources.

In certain embodiments, the vesicle may be stabilized sterically by the incorporation of polyethylene glycol (PEG), or by the PEG headgroups of a synthetic phospholipid (PEG conjugated to distearoyl phosphatidylethanolamine (DSPE), see e.g. (61)). Preferred surfactants are those with good miscibility such as Tween ™, Triton™, sodium dodecyl sulfate (SDS), sodium laurel sulfate, or sodium octylglycoside.

Preferred surfactants form micelles when added to aqueous solution above the surfactant's phase transition temperature. The surfactants may be composed of one or more aliphatic chains. These aliphatic chains may be saturated, unsaturated, or substituted in other ways, such as by ethoxylation; typically the aliphatic chain contains greater than about 12 carbons. Additional suitable surfactants include the following: lauryl-, myristyl-, linoleyl-, or stearyl-sulfobetaine; lauryl-, myristyl-, linoleyl- or stearyl-sarcosine; linoleyl, myristyl-, or cetyl- betaine; lauroamidopropyl-, cocamidopropyl-, linoleamidopropyl-, myristamidopropyl-, palmidopropyl-, or isostearamidopropyl-betaine (e.g. lauroamidopropyl); myristanidopropyl-, palmidopropyl-, or isostearamidopropyl-dimethylamine; sodium methyl cocoyl-, or disodium methyl oleyl-taurate; and the MONAQUAT series (Mona Industries, Inc., Paterson, N.J.). See also Example 4.

Preferred sterols and sterol esters suitable for use in preparing multimeric protein complexes include cholesterol, cholestanol, cholesterol sulfate, and other cholesterol analogs and derivatives. The fact that a vesicle may comprise many different lipids and detergents allows great flexibility in engineering a tethered protein-vesicle complex with desired properties. For example, one may produce vesicles that bind different number of proteins by varying the lipid composition of the starting materials to create larger vesicles, or by increasing the percentage of phosphatidylinositol lipids in the vesicle.

VII. Utilities

Generally, the modified proteins described herein are useful for treating the same medical conditions that can be treated with the unmodified forms of the proteins. However, the hydrophobically-modified proteins described herein provide several significant improvements over the unmodified forms. First, their increased potency enables treatment with smaller amounts of protein and over shorter periods of time. This will be important in both systemic and CNS applications. Secondly, replacement of the N-terminal cysteine with a less chemically reactive amino acid allows for easier production, formulation, and storage of a protein for clinical use. Thirdly, the pharmacodynamics of a protein will be altered by hydrophobic modification and this will allow the proteins to be localized in the vicinity of the site of administration, thus increasing their safety, by minimizing systematic exposure, and their effectiveness by increasing their local concentration. The proteins of the invention are also useful in diagnostic compositions and methods to detect their corresponding receptors.

As an example of the first point, it has been found that the half-life of hedgehog is very short after systemic application and that multiple injections are required to achieve a robust response to the protein. The higher potency of the modified forms and the possibility of formulation in liposomes provides a means of achieving a response with fewer treatments. For CNS applications, the higher potency provides a means to supply an adequate amount of protein in the small volumes required for direct injection into the CNS.

The importance of the second point is illustrated by the fact that we have found that the N-terminal cysteine of hedgehog is highly susceptible to chemical attack, either to form other chemical adducts or to oxidatively-dimerize with another hedgehog protein. To prevent this, special buffers and procedures are used during purification, and dithiothreitol is used in the final formulation. These precautions necessitate careful evaluation of the effects of the formulation buffer in animal models.

As an example of the third point, the more limited the range over which a protein diffuses away from the site of administration, the higher the local concentration.

This higher local concentration may therefore allow more specific clinical responses during the treatment of neurological disorders after direct injection into the desired region of the brain or spinal cord.

Similarly, the modified proteins can be administered locally to the site of bone fractures to help heal these fractures, in the gonads to treat fertility disorders, intraocularly to treat eye disorders, and under the skin to treat dermatological conditions, and to stimulate local hair growth. Localization of the hydrophobically-modified proteins to the site of administration therefore reduces possibly undesirable systemic exposure to other tissues and organs.

For therapeutic use, hydrophobically-modified proteins of the invention are placed into pharmaceutically acceptable, sterile, isotonic formulations and optionally are administered by standard means well known in the field. The formulation is preferably liquid or may be lyophilized powder. It is envisioned that a therapeutic administration of, for instance, a multimeric protein complex may comprise liposomes incorporating the derivatized proteins described herein.

It will be appreciated by persons having ordinary skill in the art that the particular administration, dosage, and clinical applications of a hydrophobically-modified protein of the invention will vary depending upon the particular protein and its biological activity.

As but one example of the application of the proteins of this invention in a therapeutic context, therapeutic hydrophobically-modified hedgehog proteins can be administered to patients suffering from a variety of neurological conditions. The ability of hedgehog protein to regulate neuronal differentiation during development of the nervous system and also presumably in the adult state indicates that hydrophobically-modified hedgehog can reasonably be expected to facilitate control of adult neurons with regard to maintenance, functional performance, and aging of normal cells; repair and regeneration processes in lesioned cells; and prevention of degeneration and premature death which results from loss of differentiation in certain pathological conditions. In light of this, the present hydrophobically-modified hedgehog compositions, by treatment with a local infusion can prevent and/or reduce the severity of neurological conditions deriving from: (i) acute, subacute, or chronic injury to the nervous system, including traumatic injury, chemical injury, vessel injury, and deficits (such as the ischemia from stroke), together with infectious and tumor-induced injury; (ii) aging of the nervous system including Alzheimer's disease; (iii) chronic neurodegenerative diseases of the nervous system, including Parkinson's disease, Huntington's chorea, amylotrophic lateral sclerosis and the like; and (iv) chronic immunological diseases of the nervous system, including multiple sclerosis. The hydrophobically-modifed protein may also be injected into the cerebrospinal fluid, e.g., in order to address deficiencies of brain cells, or into the lymph system or blood stream as required to target other tissue or organ system-specific disorders.

Hedgehog compositions of the invention may be used to rescue, for example, various neurons from lesion-induced death as well as guiding reprojection of these neurons after such damage. Such damage can be attributed to conditions that include, but are not limited to, CNS trauma infarction, infection, metabolic disease, nutritional deficiency, and toxic agents (such as cisplatin treatment). Certain hedgehog proteins cause neoplastic or hyperplastic transformed cells to become either post-mitotic or apoptotic. Such compositions may, therefore, be of use in the treatment of, for instance, malignant gliomas, medulloblastomas and neuroectodermal tumors.

The proteins may also be linked to detectable markers, such as fluoroscopically or radiographically opaque substances, and administered to a subject to allow imaging of tissues which express hedgehog receptors. The proteins may also be bound to substances, such as horseradish peroxidase, which can be used as immunocytochemical stains to allow visualization of areas of hedgehog ligand-positive cells on histological sections. Hydrophobically-modified proteins of the invention, either alone or as multivalent protein complexes, can be used to specifically target medical therapies against cancers and tumors which express the receptor for the protein. Such materials can be made more effective as cancer therapeutics by using them as delivery vehicles for antineoplastic drugs, toxins, and cytocidal radionuclides, such as yttrium 90.

A toxin may also be conjugated to hydrophobically-modified hedgehog (or vesicle-containing multivalent complexes thereof) to selectively target and kill hedgehog-responsive cells, such as a tumor expressing hedgehog receptor(s). Other toxins are equally useful, as known to those of skill in the art. Such toxins include, but are not limited to, Pseudomonas exotoxin, Diphtheria toxin, and saporin. This approach should prove successful because hedgehog receptor(s) are expressed in a very limited number of tissues. Another approach to such medical therapies is to use radioisotope labeled, hydrophobically-modified protein (or multivalent complexes thereof). Such radiolabeled compounds will preferentially target radioactivity to sites in cells expressing the protein receptor(s), sparing normal tissues. Depending on the radioisotope employed, the radiation emitted from a radiolabeled protein bound to a tumor cell may also kill nearby malignant tumor cells that do not express the protein receptor. A variety of radionuclides may be used. Radio-iodine (for example, ¹³¹I) has been successful when employed with monoclonal antibodies against CD20 present on B-cell lymphomas (63).

The protein compositions to be used in therapy will be formulated and dosages established in a fashion consistent with good medical practice taking into account the disorder to be treated, the condition of the individual patient, the site of delivery of the isolated polypeptide, the method of administration, and other factors known to practitioners. The therapeutic may be prepared for administration by mixing a protein, a protein-containing vesicle, or a derivatized complex at the desired degree of purity with physiologically acceptable carriers (i.e. carriers which are nontoxic to recipients at the dosages and concentrations employed).

It is envisioned that local delivery to the site will be the primary route for therapeutic administration of the proteins of this invention. Intravenous delivery, or delivery through catheter or other surgical tubing may also be envisioned. Alternative routes include tablets and the like, commercially available nebulizers for liquid formulations, and inhalation of lyophilized or aerosolized formulations. Liquid formulations may be utilized after reconstitution from powder formulations.

The dose administered will be dependent upon the properties of the vesicle and protein employed, e.g. its binding activity and in vivo plasma half-life, the concentration of the vesicle and protein in the formulation, the administration route, the site and rate of dosage, the clinical tolerance of the patient involved, the pathological condition afflicting the patient and the like, as is well known within the skill of the physician. Generally, doses of from about 5×10⁻⁷ to 5×10⁻⁹ Molar of protein per patient per administration are preferred, although the dosage will depend on the nature of the protein. Different dosages may be utilized during a series of sequential administrations.

The invention is also directed towards a pharmaceutical formulation which includes a hedgehog protein modified according to the invention in combination with a pharmaceutically acceptable carrier. In one embodiment, the formulation also includes vesicles.

The hydrophobically-modified hedgehog proteins of the invention are also useful in gene therapy methods.

For neurodegenerative disorders, several animal models are available that are believed to have some clinical predicative value. For Parkinson's disease, models involve the protection, or the recovery in rodents or primates in which the nigral-striatal dopaminergic pathway is damaged either by the systemic administration of MPTP or the local (intracranial) administration of 6-hydroxydopamine [6-OHDA], two selective dopaminergic toxins. Specific models are: MPTP-treated mouse model (64); MPTP-treated primate (marmoset or Rhesus) model (65), and the unilateral 6-OHDA lesion rat model (66). For ALS, (Amyotrophic lateral sclerosis) models involve treatment of several mice strains that show spontaneous motor neuron degeneration, including the wobbler (67) and pmn mice (68), and of transgenic mice expressing the human mutated superoxidase dismutase (hSOD) gene that has been linked to familial ALS (69). For spinal cord injury, the most common models involve contusion injury to rats, either through a calibrated weight drop, or fluid (hydrodynamic) injury (70). For Huntington's, models involve protection from excitotoxin (NMDA, quinolinic acid, kainic acid, 3-nitro-propionic acid, APMA) lesion to the striatum in rats (71, 72). Recently, a model of transgenic mice overexpressing the human trinucleotide expanded repeat in the huntingtin gene has also been described (73). For multiple sclerosis, EAE in mice and rats is induced by immunization with MBP (myelin basic protein), or passive transfer of T cells activated with MBP (74). For Alzheimer's, a relevant murine model is a determination of protection against lesion of the fimbria-fornix in rats (septal lesion), the main nerve bundle supplying the cholinergic innervation of the hippocampus (75), as well as use of transgenic mice overexpressing the human beta-amyloid gene. For peripheral neuropathies, a relevant model is protection against loss of peripheral nerve conductance caused by chemotherapeutic agents such as taxol, vincristine, and cisplatin in mice and rats (76).

This invention will now be described more fully with reference to the following, non-limiting, Examples.

EXAMPLE 1 Human Sonic Hedgehog is Lipid-Modified when Expressed in Insect Cells

A. Expression of Human Sonic Hedgehog

The cDNA for full-length human Sonic hedgehog (Shh) was provided as a 1.6 kb EcoRI fragment subcloned into pBluescript SK⁺ (20). The 5′ and 3′ NotI sites immediately flanking the Shh open reading frame were added by unique site elimination mutagenesis using a Pharmacia kit following the manufacturer's recommended protocol. The 1.4 kb NotI fragment carrying the full-length Shh cDNA was then subcloned into the insect expression vector, pFastBac (Life Technologies, Inc.). Recombinant baculovirus was generated using the procedures supplied by Life Technologies, Inc. The resulting virus was used to create a high titer virus stock. Methods used for production and purification of Shh are described below. The presence of membrane-associated Shh was examined by FACS and by Western blot analysis. Peak expression occurred 48 h post-infection. For Western blot analysis, supernatants and cell lysates from Shh-infected or uninfected cells were subjected to SDS-PAGE on a 10-20% gradient gel under reducing conditions, transferred electrophoretically to nitrocellulose, and the Shh detected with a rabbit polyclonal antiserum raised against an N-terminal Shh 15-mer peptide-keyhole limpet hemocyanin conjugate. The cell lysates were made by incubating the cells for 5 min at 25° C. in 20 mM Na₂HPO₄ pH 6.5, 1% Nonidet P-40 and 150 mM NaCl or 20 mM Tris-HCl pH 8.0, 50 mM NaCl, 0.5% Nonidet P-40 and 0.5% sodium deoxycholate and then pelleting particulates at 13,000 rpm for 10 min at 4° C. in an Eppendorf centrifuge.

B. Purification of Membrane-Tethered Human Sonic Hedgehog

The membrane-tethered form of Shh was produced in High Five™ insect cells (Invitrogen) using the recombinant baculovirus encoding full-length Shh discussed above. High Five™ cells were grown at 28° C. in sf900 II serum free medium (Life Technologies, Inc.) in a 10 L bioreactor controlled for oxygen. The cells were infected in late log phase at ca. 2×10⁶ cells/mL with virus at a MOI of 3 and harvested 48 h after infection (cell viability at the time of harvest was >50%). The cells were collected by centrifugation and washed in 10 mM Na₂HPO₄ pH 6.5, 150 mM NaCl pH plus 0.5 mM PMSF. The resulting cell pellet (150 g wet weight) was suspended in 1.2 L of 10 mM Na₂HPO₄ pH 6.5, 150 mM NaCl, 0.5 mM PMSF, 5 μM pepstatin A, 10 μg/mL leupeptin, and 2 μg/mL E64, and 120 mL of a 10% solution of Triton X-100 was then added.

After a 30 min incubation on ice, particulates were removed by centrifugation (1500×g, 10 min). All subsequent steps were performed at 4-6° C. The pH of the supernatant was adjusted to 5.0 with a stock solution of 0.5 M MES pH 5.0 (50 mM final) and loaded onto a 150 ml SP-Sepharose Fast Flow column (Pharmacia). The column was washed with 300 mL of 5 mM Na₂HPO₄ pH 5.5, 150 mM NaCl, 0.5 mM PMSF, 0.1% Nonidet P-40, then with 200 mL of 5 mM Na₂HPO₄ pH 5.5, 300 mM NaCl, 0.1% Nonidet P-40, and bound hedgehog eluted with 5 mM Na₂HPO₄ pH 5.5, 800 mM NaCl, 0.1% Nonidet P-40.

The Shh was next subjected to immunoaffinity chromatography on 5E1-Sepharose resin that was prepared by conjugating 4 mg of antibody per mL of CNBr activated Sepharose 4B resin. The SP-Sepharose elution pool was diluted with two volumes of 50 mM HEPES pH 7.5 and batch loaded onto the 5E1 resin (1 h). The resin was collected in a column, washed with 10 column volumes of PBS containing 0.1% hydrogenated Triton X-100 (Calbiochem), and eluted with 25 mM NaH₂PO₄ pH 3.0, 200 mM NaCl, 0.1% hydrogenated Triton X-100. The elution fractions were neutralized with 0.1 volume of 1M HEPES pH 7.5 and analyzed for total protein content from absorbance measurements at 240-340 nm and for purity by SDS-PAGE. Fractions were stored at −70° C.

Peak fractions from three affinity steps were pooled, diluted with 1.3 volumes of 50 mM HEPES pH 7.5, 0.2% hydrogenated Triton X-100 and again batch loaded onto the 5E1 resin. The resin was collected in a column, washed with three column volumes of PBS pH 7.2, 1% octylglucoside (US Biochemical Corp.), and eluted with 25 mM NaH₂PO₄ pH 3.0, 200 mM NaCl, 1% octylglucoside. The elution fractions were neutralized and analyzed as described above, pooled, filtered through a 0.2 micron filter, aliquoted, and stored at −70° C.

When full-length human sonic hedgehog (Shh) was expressed in High Five™ insect cells, over 95% of the N-terminal fragment was detected by Western blotting in a form that was cell-associated. By SDS-PAGE, the purified protein migrated as a single sharp band with apparent mass of 20 kDa (FIG. 1, lane c). The protein migrated faster by about 0.5 kDa than a soluble version of the protein that had been produced in E.coli (FIG. 1, lanes b-d), consistent with data published previously (19). Similarly as described (19), the soluble and membrane-bound Shh proteins were also readily distinguishable by reverse phase HPLC where the tethered form eluted later in the acetonitrile gradient. The concentration of acetonitrile needed for elution of the membrane-bound form was 60% versus only 45% with the soluble form, indicating a significant increase in the hydrophobicity of the protein.

C. Mass Spectrometry Analysis of Membrane-Tethered Human Sonic Hedgehog

Aliquots of Shh were subjected to reverse phase HPLC on a C₄ column (Vydac, Cat. No. 214TP104, column dimensions 4.6 mm internal diameter×250 mm) at ambient temperature. Bound components were eluted with a 30 min 0-80% gradient of acetonitrile in 0.1% trifluoroacetic acid at a flow rate of 1.4 mL/min. The column effluent was monitored at 280 nm and 0.5 min fractions were collected. 25 μL aliquots of fractions containing protein were dried in a Speed Vac concentrator, dissolved in electrophoresis sample buffer, and analyzed by SDS-PAGE. Hedgehog-containing fractions were pooled, concentrated 4-fold in a Speed Vac concentrator and the protein content assayed by absorbance at 280 nm using an extinction coefficient of 1.33 for a 1 mg/mL solution of Shh. Samples were subjected to ESI-MS on a Micromass Quattro II triple quadrupole mass spectrometer, equipped with an electrospray ion source. A volume of 6 μL of HPLC-purified hedgehog was infused directly into the ion source at a rate of 10 μL/min using 50% water, 50% acetonitrile, 0.1% formic acid as the solvent in the syringe pump. Scans were acquired throughout the sample infusion. All electrospray mass spectral data were acquired and stored in profile mode and were processed using the Micromass MassLynx data system.

Peptides from an endoproteinase Lys-C digest of pyridylethylated-Shh were analyzed by reverse phase HPLC in line with the Micromass Quattro II triple quadrupole mass spectrometer. The digest was separated on a Reliasil C₁₈ column using a Michrom™ ultrafast Microprotein Analyzer system at a flow rate of 50 μL/min with a 5-85% acetonitrile gradient in 0.05% trifluoroacetic acid. Scans were acquired from m/z 400-2000 throughout the run and processed as described above.

Sequencing of the N-terminal peptide from tethered Shh was performed by Post Source Decay (PSD)-measurement on a Voyager-DE™ STR (PerSeptive Biosystems, Framingham, Mass.) time-of-flight (TOF) mass spectrometer using α-cyano-4-hydroxycinnamic acid as the matrix (22,23). Exactly 0.5 μL of HPLC-purified endoproteinase Lys-C peptide was mixed with 0.5 μL of matrix on the target plate. To cover the entire spectrum of fragment ions, the mirror voltages were decreased from 20 to 1.2 kv in 11 steps.

Electrospray ionization mass spectrometry data for the soluble and membrane-bound forms of Shh showed primary species with masses of 19560 and 20167 Da, respectively (FIG. 2). The measured mass of 19560 Da matches the predicted mass for Shh starting with Cys-1 and terminating with Gly-174 (calc. mass of 19560.02 Da). In contrast, the 20167 Da mass did not agree with any available prediction nor could the difference in the masses of the tethered and soluble forms, 607 Da, be accounted for by any known modification or by aberrant proteolytic processing. Previously, Porter et al. (18) demonstrated that Drosophila hedgehog contained a cholesterol moiety and thus it was possible that the mass difference in the human system was due, at least in part, to cholesterol (calculated mass for esterified cholesterol is 368.65 Da). The presence of a minor component in the mass spectrum of tethered Shh at 19796 Da, which differs from the primary peak by 371 Da, supported this notion.

Further evidence for cholesterol was obtained by treating the tethered Shh with a mild alkali under conditions that can break the cholesterol linkage without disrupting peptide bonds (18), and then reanalyzing the reaction products by mass spectrometry (MS). Briefly, insect cell-derived Shh was treated with 50 mM KOH, 95% methanol for 1 h at ambient temperature and then analyzed by ESI-MS or digested with endoproteinase Lys-C and subjected to LC (liquid chromatography)-MS on the Micromass Quattro II triple quadrupole mass spectrometer. For samples subjected to LC-MS, the proteins were first treated with 4-vinylpyridine. Base treatment shifted the mass by 387 Da, which is consistent with the loss of cholesterol plus water (see Table 3). The mass of soluble Shh was not affected by base treatment. Together, these observations suggested that the membrane-tethered human Shh contained two modifications, a cholesterol and a second moiety with a mass of 236 Da. The similarity in mass between this value and the mass of an added palmitoyl group (238 Da) suggested that the protein might be palmitoylated. More accurate estimates of the mass, discussed below, revealed a correlation within 0.1 Da of the predicted mass of a palmitoyl moiety.

TABLE 3 Characterization of tethered Shh by MS. Calculated mass values were determined using average residue masses in part a and monoisotopic protonated masses in part b. Mass (Da) Protein Calculated Measured a. KOH-treated Shh no tether (−treatment) 19560.02 19560 no tether (+treatment) 9560.02 19561 tethered (−treatment) 20167.14 20167 tethered (+treatment) 19798.49 19780 b. N-terminal endoproteinase Lys-C peptide(MH⁺)* no tether 983.49 983.50 tethered 1221.72 1221.79 *All mass values for peptides described herein are protonated masses

Subsequently, we determined that tethered Shh could be fractionated into subspecies by HPLC with a modified elution gradient and we developed a simple HPLC assay for quantifying the various forms. Results from these analyses are shown in FIG. 3. In this assay, the unmodified Shh elutes first (peak 1), then cholesterol-modified Shh elutes (peak 2), and finally product containing both cholesterol and palmitic acid-modified Shh elutes (peak 3). The complex shape of peak 3 reflects the presence of a modified form of the pahnitoyl group that was identified through sequencing by MALDI PSD measurement. The variant was 2 Da smaller than predicted and may therefore contain an unsaturated bond (data not shown).

D. Localization of the Palmitic Acid Modification Within the Human Sonic Hedgehog Sequence

The site of palmitoylation within the human sequence was identified using a combination of peptide mapping and sequence analysis. FIG. 4B shows results from a peptide mapping analysis of the soluble protein with an LC-MS readout. Mass data accounting for over 98% of the soluble Shh sequence could be accounted for from the analysis. The peak noted with an asterisk corresponds to the N-terminal peptide (residues 1-9 plus 4-vinylpyridine, observed mass 983.50 Da, calculated mass 983.49 Da; Table 3). In the corresponding analysis of the tethered product (FIG. 4A), this peptide was missing and instead a more hydrophobic peptide with mass of 1221.79 Da was observed (noted with asterisk).

The 1221.79 Da moiety is consistent with the presence of a modified form of the N-terminal peptide, i.e. 983.49 Da for the peptide component plus 238.23 Da. The 1221.79 Da peptide was next subjected to sequence analysis by MALDI PSD measurement. The resulting PSD spectrum is shown in FIG. 5. Ions corresponding to b1, b2, b4, b5, b8+H₂O, y8, y7, y5, y4, y3, y2, and y1 fragments were detected which confirmed the sequence. In addition, the b1 and b2 ions indicated that the pyridylethylated Cys-1 adduct was palmitoylated. Only ions containing Cys-1, contained the added 238.23 Da mass.

Since cysteine is a normal site of palmitoylation for proteins in vivo, it was not surprising to find the novel adduct attached to the N-terminal cysteine. However, two pieces of evidence suggested that the lipid was attached to the amino group on the cysteine and not the thiol. First, in the peptide mapping study, we used 4-vinylpyridine as a spectroscopic tag to monitor free thiol groups (27). Pyridylethylation is highly specific for cysteine thiols and adds a 105 Da adduct that can be detected by MS. The observed Cys-1-containing fragments in the PSD spectrum contained both palmitoyl and pyridylethyl modifications, implying the presence of a free thiol group. Second, the tethered Shh was subjected to automated N-terminal Edman sequencing and no sequence was obtained, suggesting blockage at the N-terminal α-amine. By contrast, the corresponding soluble form of Shh can be sequenced readily.

EXAMPLE 2 Human Sonic Hedgehog can be Modified with Palmitic Acid in a Cell-Free System

Soluble Shh was labeled with ³H-palmitic acid in a cell-free system using a modified version of a published procedure (24). A crude microsomal fraction from rat liver was prepared by subjecting a liver homogenate to sequential centrifugation at 3000×g for 10 min, 9000×g for 20 min, and 100,000×g for 30 min. The 100,000×g pellet was suspended in 10 mM HEPES pH 7.4, 10% sucrose and again centrifuged at 100,000×g for 20 min. The final pellet (derived from 10 g of liver) was suspended in 3 mL of 20 mM Tris-HCl pH 7.4, 150 mM NaCl, 1 mM EDTA, 10 μg/mL leupeptin, 0.15% Triton X-100, aliquoted, and stored at −70° C. Reactions containing 3 μg Shh, 1 μL of rat microsomes, 50 ng/mL Coenzyme A (Sigma), 0.3 mM ATP, 20 mM Tris-HCl pH 7.4, 150 mM NaCl, 1 mM EDTA, 10 μg/mL leupeptin, and 0.5 μCi-[9,10-³H]-palmitic acid (50 Ci/mmol; New England Nuclear) were performed at room temperature for 1 h. Reactions were stopped with reducing electrophoresis sample buffer, subjected to SDS-PAGE on a 10-20% gradient gel, and visualized by fluorography.

As shown in FIG. 1 (lane e), Shh is readily labeled with the radioactive tracer. None of the ca. hundred other proteins in the reaction mixture were labeled (see the corresponding Coomassie blue-stained gel profile in lane j), indicating a high degree of specificity of the palmitoylation reaction. As further evidence for the specificity of the palmitoylation reaction, we tested two Shh variants in which the site of palmitoylation had been eliminated. FIG. 1 (lane f) shows results from the analysis of a truncated form of soluble Shh that was lacking the first 10 amino acid residues of the mature sequence) and lane g, of a mutant form of Shh containing, at its N-terminal end, a single Cys-1 to Ser point mutation. Neither of the variants were labeled.

The significance of the N-terminal cysteine as the site of lipid derivatization is highlighted by the fact that wild type soluble Shh is readily labeled while the N-terminal cysteine to serine mutant is not. The inability to label the N-terminal serine mutant argues against a simple reaction mechanism where the palmitoyl moiety is directly attached to the N-terminal α-amine since under the test conditions the serine should have substituted for the cysteine.

We also tested the role of the free N-terminus using a form of soluble Shh with an N-terminal histidine (His)-tag extension. The soluble human Shh used in these studies had been produced initially as a His-tagged fusion protein with an enterokinase cleavage site at the junction of the mature sequence and was then processed with enterokinase to remove the His tag. The His-tagged Shh was not palmitoylated despite the presence of the free thiol group of the cysteine (See FIG. 1, lane i). While we cannot rule out the possibility that the N-terminal extension sterically inhibits palmitoylation from occurring, Cys-1 is at the P1′ position of the enterokinase cleavage site and is readily accessible to enzymatic processing. Thus it appears that both the thiol and α-amine of Cys-1 contribute to the palmitoylation reaction. Since all known palmitoylation reactions target the side chains of Cys, Ser, or Thr residues, we infer that the modification on hedgehog starts with the formation of a thioester intermediate, and that the palmitoyl moiety is then transferred to the N-terminus through the formation of a cyclic intermediate. This hypothesis was confirmed during studies of the modification of human Sonic hedgehog using palmityol Coenzyme A (See Example 8).

EXAMPLE 3 Demonstration of Increased Potency of Naturally Ocurring Fatty-Acylated Human Sonic Hedgehog in a Cell-Based (C3H10T1/2) Assay

Shh was tested for function in a cell-based assay measuring alkaline phosphatase induction in C3H10T1/2 cells (25) with a 5 day readout. The assay was preformed in a 96-well format. Samples were run in duplicate. For tethered Shh (100 μg/mL), the samples were first diluted 200-fold with normal growth medium then subjected to serial 2-fold dilutions down the plates. Wells were normalized for potential effects of the added octylglucoside by including 0.005% octylglucoside in the culture medium. Blocking studies using the neutralizing murine mAb 5E1 (26) were performed by mixing Shh with serial dilutions of the antibody for 30 min at ambient temperature in culture medium prior to adding the test samples to the plates.

In this assay, soluble human Shh produces a dose-dependent response with an IC₅₀ of 1 μg/mL and a maximal signal at 3 μg/mL (FIG. 6A). Tethered human Shh, with a cholesterol attached at the C-terminus and a palmitoyl group at the N-terminus, similarly produced a dose-dependent response in the assay but with an IC₅₀ of 0.03 μg/mL and a maximal signal at 0.1 μg/mL, indicating that it was about 30 times as potent as soluble Shh. To verify that the observed activity was hedgehog specific, we tested whether the activity could be inhibited with the anti-hedgehog neutralizing mAb 5E1. Both soluble and tethered Shh were inhibited by 5E1 treatment (FIG. 6B). Inhibition of the tethered Shh required a tenth as much 5E1 consistent with its increased activity in the assay.

Tethered Shh was tested in a receptor binding assay, monitoring its ability to bind patched, using a modified version of a recently published assay (10). The tethered Shh showed dose-dependent binding to cells expressing patched with an apparent IC₅₀ of 400 ng/mL (FIG. 7). In the same assay, soluble Shh bound to patched with an apparent IC₅₀ of 150 ng/mL, indicating that the tethered form bound only slightly less tightly to its receptor.

EXAMPLE 4 Analysis of Tethered Human Sonic Hedgehog after Reconstitution into Liposomes

This example illustrates that reconstitution experiments into positively and negatively charged liposomes by detergent dilution over a wide range of lipid: protein ratios (w/w) from 1:1 to 100:1 had no effect on tethered Shh activity in the C3H10T1/2 assay.

Reconstitution into phospholipid-containing liposomes provides a useful formulation for lipid-containing proteins because it allows a lipid-containing protein to exist in a near normal setting. To test whether such a formulation was viable for tethered Shh we utilized a detergent dilution method to incorporate the protein into a liposome (60), where preformed liposomes are mixed with octylglucoside and the protein of interest, and then the detergent is diluted below its critical micelle concentration, thus driving the reconstitution. While any of a large number of pure or lipid mixtures can be utilized, we selected two commercially available mixtures as models; a negatively charged liposome kit containing egg L-α-phosphatidylcholine, dicetyl phosphate, and cholesterol (Cat. No. L-4262; Sigma, St. Louis, Mo.), and a positively charged liposome kit consisting of egg phosphatidyl choline, stearlyamine, and cholesterol (Cat. No L-4137, Sigma).

Briefly, the lipids were transferred into a Pyrex tube, dried under a stream of nitrogen, and residual solvent removed by lyophilization. The lipid was suspended in 10 mM HEPES pH 7.5, 100 mM NaCl, 2.0% octylglucoside, vortexed, and sonicated until the suspension had turned opalescent in appearance. The lipid was then filtered through a 0.2 micron filter. Aliquots of tethered Shh, from baculovirus-infected High Five™ insect cells, in octylglucoside were treated with a 400-, 1000-, 5000-, and a 20000-fold excess of lipid (w/w) and after a 15 min preincubation the samples were diluted and assayed for activity in the C3H10T1/2 assay.

Neither the positive nor the negative liposome treatment had any affect on the activity of the hedgehog indicating that a lipid carrier was a viable formulation. To verify that the hedgehog indeed had become reconstituted, parallel samples were subjected to centrifugation under conditions where the tethered Shh would normally pellet and the liposomes would float to the surface of the sample. Under these conditions the tethered Shh floated to the surface, indicating that reconstitution had occurred.

EXAMPLE 5 Characterization of Membrane-Tethered Human Sonic Hedgehog from Mammalian (EBNA-293) Cells

In order to assess whether palmitoylation was a general modification pathway for Sonic hedgehog or whether it was specific to insect cell production, the protein was also produced in a mammalian system in EBNA-293 cells. For expression of full-length Shh in mammalian cells, the 1.4 kb NotI fragment containing full-length Shh (See Example 1) was cloned into a derivative of the vector, CH269 pCEP4 (Invitrogen, San Diego, Calif. (21)). The construct was transfected into EBNA-293 cells using lipofectamine (Life Technologies, Inc.) and the cells were harvested 48 h post-transfection. The expression of surface Shh was verified by FACS and by Western blot analysis.

Tethered Shh from EBNA-293 cells was fractionated by reverse phase HPLC on a narrow bore C₄ column (See FIG. 3). Peaks were analyzed by ESI-MS (parts a and b of Table 4) or by MALDI-TOF MS on a Finnigan LaserMat mass spectrometer using α-cyano-4-hydroxycinnamic acid as the matrix (part c of Table 4). By SDS-PAGE, the protein migrated slightly faster than soluble Shh, it was retarded on the C₄ column in the reverse phase HPLC analysis, and, by mass spectrometry, it contained an ion corresponding to the palmitic acid plus cholesterol modification. However, unlike the insect cell-derived product where over 80% of the product contained both the palmitic acid and cholesterol modification, the HPLC elution profile and data from mass spectrometry revealed that most of the mammalian cell-derived protein lacked the palmitoyl moiety (see Table 4 and FIG. 3C). That is, in peak 2 from EBNA-293 cells the ratio of clipped (des-1-10) versus intact protein by MS signal was 50% whereas for peak 1 only about 10% of the Shh was clipped. Interestingly, both the insect cell and mammalian cell-derived products showed comparable activity in the C3H10T1/2 assay suggesting that both the cholesterol, and the cholesterol plus palmitic acid modifications are functional. Whether the second lipid attachment site is used simply to further stabilize the association of the protein with membrane or whether it plays a more active role and affects its con formation or protein-protein contacts remains to be determined.

Fatty acid derivatization of proteins is a common post translational modification that occurs late in the maturation processes (28,29). For cysteine derivatives, the process is dynamic involving separate enzymes that add and remove the modification on the sulfhydryl group. The most common functions of such derivatization (e.g., palmitoylation) are to alter the physico-chemical properties of the protein, i.e., to target a protein to its site of function, to promote protein-protein interactions, and to mediate protein-membrane interactions (30). For hedgehog, while the difference in the extent of palmitoylation in the insect and mammalian cell-derived preparations (80% in insect cells versus 30% in mammalian cells) was surprising, we do not know if it is biologically significant or whether it simply reflects differences in the cellular machinery of the two test systems for adding and removing palmitic acid. The difference in the extent of modification in the insect and mammalian cells is unlikely to be species related since tethered Drosophila hedgehog that was produced in insect cells lacked palmitic acid (19) despite having the identical N-terminal sequence.

TABLE 4 Mass spectrometry analysis of EBNA-293-derived tethered human Sonic hedgehog. Mass (Da) Protein Calculated Measured a. bacterial expressed (no tether) 19560.02 19560 b. baculovirus expressed (tethered) +palmitic acid 19798.49 19796 +palmitic acid/cholesterol 20167.14 20168 c. EBNA-293 cell expressed (tethered) peak 1 (9% of total hedgehog) no tether 19560.02 19581 no tether (des 1-9) 18700.02 18712 peak 2 (61% of total hedgehog) +cholesterol 19928.67 19934 +cholesterol (des 1-10) 18912.48 18889 peak 3 (30% oftotal hedgehog) +palmitoyl/cholesterol 20167.14 20174

EXAMPLE 6 Lipid Modifications of Rat Sonic Hedgehog

This Example illustrates that a variety of lipids become linked to a soluble version of rat Sonic hedgehog when the rat Shh gene encoding residues 1-174 is expressed in High Five™ insect cells, essentially as for the full-length human Shh described in Example 1. The lipid modification renders this fraction membrane-associated. The N-terminal fragment (residues 1-174 of unprocessed rat Sonic hedgehog) differs by only 2 amino acid residues to that of the N-terminal fragment of human Sonic hedgehog. In the rat Sonic hedgehog N-terminal fragment, threonine replaces serine at position 44, and aspartic acid replaces glycine at position 173. When rat Sonic hedgehog lacking the autoprocessing domain is expressed in the High-Five™ insect cell/baculovirus expression system, the majority of the protein is secreted into the culture medium since it lacks the ability to attach a cholesterol moiety to the C-terminus. This soluble form has a specific biological activity (measured by the C3H10T1/2 alkaline phosphatase induction assay of Example 3) that was similar to that of the soluble, N-terminal fragment of human Sonic hedgehog expressed and purified from E. coli.

However, a small fraction of the total protein remains associated with the insect cells. The cell-associated rat Sonic hedgehog protein was purified essentially as described in Example 1, and was found to be significantly more active in the alkaline phosphatase assay (data not presented) than the soluble, N-terminal fragments of either human or rat Sonic hedgehog purified from E. coli and the High-Five™ insect cell/baculovirus expression system, respectively. Subsequent analyses of the rat Sonic hedgehog N-terminal fragments by HPLC and electrospray mass spectrometry (as described in Example 1) suggests that the protein is lipid-modified and that there was more than one type of lipid modification. Supporting evidence includes the following observations:

1. The cell-associated forms elute later than the soluble, N-terminal fragments of human and rat sonic hedgehog from a C₄ reverse phase HPLC column (Vydac catalog number 214TP104) developed with a linear 30 min 0-70% acetonitrile gradient in 0.1% trifluoroacetic acid;

2. The masses of the cell-associated forms are consistent with that expected for the lipid-modified proteins, as shown in Table 5.

TABLE 5 Masses of various lipid-modified forms of rat Sonic hedgehog. Expected Protein (MH⁺) Adduct Mass* (MH⁺) Observed Mass unmodified none 19,632.08 19,632 myristoyl- CH₃(CH₂)₁₂CO- 19,842.50 19,841 palmitoyl- CH₃(CH₂)₁₄CO- 19,870.55 19,868 stearol- CH₃(CH₂)₁₆CO- 19,898.60 19,896 arachidoyl- CH₃(CH₂)₁₈CO- 19,926.66 19,925 *Average masses were used in calculating the expected masses

The location of the lipid moiety was determined using a combination of sequence analysis and peptide mapping. Automated N-terminal Edman sequencing of the lipid-modified forms indicated that the N-terminus was blocked, suggesting that the lipid was attached to the α-amine of the N-terminal cysteine. Endo-Lys-C peptide mapping, MALDI-TOF mass spectrometry and MALDI PSD analysis (as described in Example 1) of the 4-vinylpyridine alkylated lipid-modified forms, were used to confirm the location of the lipid modifications and to determine their exact masses.

The masses of the N-terminal peptides (residues 1-9 inclusive plus 4-vinylpyridine attached to the thiol side chain of the N-terminal cysteine) carrying the lipid modifications were consistent within 0.1 Da with that expected for the lipid-modified peptides as shown in Table 6.

TABLE 6 Masses of the N-terminal peptides iosolated from various lipid-modified forms of rat Sonic hedgehog. Expected Protein (MH⁺) Adduct Mass* (MH ⁺) Observed Mass myristoyl- CH₃(CH₂)₁₂CO- 1193.69 1193.76 palmitoyl- CH₃(CH₂)₁₄CO- 1221.72 1221.65 stearoyl- CH₃(CH₂)₁₆CO- 1249.75 1249.71 *Monoisotopic masses were used in calculating the expected masses

In addition to the lipid-modified peptides shown in Table 6, peptides with masses of 1191.74, 1219.84 and 1247.82 were also detected. These masses are consistent with unsaturated forms of myristate, palmitate and stearate, respectively, although the position of the double bond in the alkyl chain was not determined. These observations indicate that both saturated and unsaturated fatty acids can be attached covalently to the N-terminal cysteine. For both the saturated and unsaturated lipid-modified peptides, MALDI PSD analysis as described in Example 1 confirmed that the lipids were attached covalently to the N-terminal cysteine residue.

EXAMPLE 7 Lipid Modification of Indian Hedgehog

To assess whether the palmitoylation reaction was unique to human Shh or whether it might occur on other hedgehog proteins, we tested whether human Indian hedgehog (expressed in E. coli as a His-tagged fusion protein with an enterokinase cleavage site immediately adjacent to the start of the mature sequence, and purified exactly as for recombinant human Sonic hedgehog (See Example 9)) could be palmitoylated using the assay described in Example 2. Human Indian hedgehog was modified (See FIG. 1, lane h), indicating that palmitoylation is likely to be a common feature of hedgehog proteins. The ability to directly label Shh and Ihh with radioactive palmitic acid in a cell-free system provided a simple screen for amino acids involved in the modification reaction. Moreover, Indian hedgehog palmitoylated by the method described in Example 8 was significantly more potent in the C3H10T1/2 assay than the unmodified Ihh.

EXAMPLE 8 Lipid Modifications of Sonic Hedgehog using Acyl-Coenzyme A

The in vitro acylation of a protein containing an N-terminal cysteine can be accomplished via a two-step, chemical reaction with a fatty acid-thioester donor. In the first step, the acyl group of the thioester donor transfers to the sulfhydryl of the N-terminal cysteine on the protein by a spontaneous transesterification reaction. Subsequently, the acyl moiety undergoes a S to N shift to the α-amine of the N-terminal cysteine to form a stable amide bond. Direct acylation of an amine function on a protein may also occur with prolonged incubation with a thioester, but the presence of a cysteine on the protein will accelerate the reaction and allow control over the acylation site. In the present examples, commercially available Coenzyme A derivatives (Sigma Chemical Company, St. Louis Mo.) are utilized, but other thioester groups would also achieve the same result. In fact, certain thioester leaving groups, such as thiobenzyl esters, would be expected to react more rapidly. Internal cysteine residues may also promote acylation to neighboring lysines (i.e., as in an internal cysteine-lysine pair) and this can be conveniently tested using synthetic peptides. Secondary acylations occuring on a protein during reaction with thioesters may be prevented by controlling the buffer composition, pH, or by site-directed mutagenesis of the neighboring lysines.

In preliminary analysis of the effect of acylation on the ability of human Sonic hedgehog to induce alkaline phosphatase in C3H10T1/2 cells, reaction mixtures contained 1 mg/mL human Sonic hedgehog (51 μM), 500 μM of the particular, commercially available, acyl-Coenzyme A (compounds tested included acetyl-CoA (C2:0), butyryl-CoA (C4:0), hexanoyl-CoA (C6:0), octanoyl-CoA (C8:0), decanoyl-CoA (C10:0), lauroyl-CoA (C12:0), myristoyl-CoA (C14:0), palmitoyl-CoA (C16:0), palmitoleoyl-CoA (C16:1), stearoyl-CoA (C18:0), arachidoyl-CoA (C20:0), behenoyl-CoA (C22:0), lignoceroyl-CoA (C24:0), succinyl-CoA, and benzoyl-CoA), 25 mM DTT, and 50 mM Na₂HPO₄ pH 7.0. The reactions were incubated at room temperature for 3 h and then analyzed immediately (without purification) for bioactivity in the C3H10T1/2 assay as described in Example 3. Samples for analysis by reverse phase HPLC and other physical methods were usually stored at −70° C. HPLC analysis was carried out on a Vydac C₄ reverse phase column (4.6 mm internal diameter×250 mm, 5 micron particle) with a 40 min gradient of 5% acetonitrile to 85% acetonitrile in aqueous 0.1% TFA, at a flow rate of 1 mL/min. The effluent was monitored at 280 nm, and fractions were collected in some experiments and analyzed for hedgehog protein on SDS-PAGE with detection by Coomassie staining and by Western blotting.

Comparison of the activity of the various reaction mixtures (FIG. 10) indicates that a chain length of between 12 and 18 carbons is optimal in inducing high alkaline phosphatase activity as compared to the unmodified protein. Increasing the chain length further resulted in an apparent reduction in activity, and the presence of a double bond in the unsaturated palmitoleoyl-CoA (C16:1) gave the same activity as the fully saturated palmitoyl-CoA (C16:0). Upon reverse phase HPLC analysis of the reaction mixtures, we observed that many of the shorter chain length acyl-CoA derivatives had not reacted with the hedgehog protein, and therefore the dependence of biological activity shown in FIG. 10 was not a true reflection of the acyl chain length.

In order to obtain data on the true activity of the modified proteins, and on the dependence of activity on acyl chain length, we developed methods for the synthesis and purification of the individual N-terminal acylated forms. Palmitoylated, myristoylated, lauroylated, decanoylated, and octanoylated human Sonic hedgehog proteins, carrying a single acyl chain attached to the α-amine of the N-terminal cysteine, were produced in reaction mixtures containing 0.80 mg/mL (41 μM) human Sonic hedgehog, 410 μM (10-fold Molar excess) of either pahnitoyl-CoA, myristoyl-CoA, or lauroyl-CoA, or 4.1 mM (100-fold Molar excess) of either decanoyl-CoA or octanoyl-CoA, 25 mM DTT (for reaction mixtures containing palmitoyl-CoA, myristoyl-CoA, or lauroyl-CoA) or 0.5 mM DTT (for reaction mixtures containing decanoyl-CoA or octanoyl-CoA), and 40 mM Na₂HPO₄ pH 7.0. Reaction mixtures were incubated at 28° C. for 24 h. Reaction of the N-terminal cysteine with the acyl thioesters results in the transfer of the acyl group to the sulfhydryl by a spontaneous transesterification reaction, which is followed by a S to N shift to the α-amine to form a stable amide linkage. The free sulfhydryl then undergoes a second transesterification reaction, yielding a protein with a fatty acyl group attached via a thioester linkage to the sulfhydryl. The thioester-linked acyl group was removed by adding consecutive 0.11 volume of 1 M Na₂HPO₄ pH 9.0, and 0.11 volume of 1 M hydroxylamine (0.1 M final concentration) followed by incubation at 28° C. for 18 h, which leaves only the acyl amide attached to the protein (62). 0.25 volume of 5% octylglucoside was then added (1% final concentration) and the mixture incubated for 1 h at room temperature. The proteins were then purified in the presence of 1% octylglucoside using SP-Sepharose Fast Flow (Pharmacia) and Bio Scale S (Biorad) cationic ion exchange chromatographies. The purified proteins were dialyzed against 5 mM Na₂HPO₄ pH 5.5, 150 mM NaCl, 1% octylglucoside, 0.5 mM DTT, and were stored at −70° C. The presence of octylglucoside was required to maintain full solubility; removal of the detergent by dilution and dialysis resulted in a 75%, 41%, and 15% loss of the palmitoylated, myristoylated, and lauroylated proteins, respectively. ESI-MS of the HPLC-purified proteins confirmed their integrity: palmitoylated Sonic hedgehog, measured mass=19798, calculated mass=19798.43; myristoylated Sonic hedgehog, measured mass=19770, calculated mass=19770.33; lauroylated Sonic hedgehog, measured mass=19742, calculated mass=19742.33; decanoylated Sonic hedgehog, measured mass=19715, calculated mass=19714.28; octanoylated Sonic hedgehog, measured mass=19686, calculated mass=19686.23.

Analysis of the various acylated forms of human Sonic hedgehog in the C3H10T1/2 assay (FIG. 11) indicated that the activity of the proteins was dependent upon the chain length. The palmitoylated, myristoylated, and lauroylated proteins showed approximately equal activity with EC₅₀ values of 5-10 ng/mL (100-200-fold increase in potency as compared to the unmodified protein). Decanoylated human Sonic hedgehog, with an EC₅₀ value of 60-70 ng/mL (15-30-fold increase in potency as compared to the unmodified protein), was less active than the palmitoylated, myristoylated, and lauroylated forms, while the octanoylated form was the least active with an EC₅₀ of 100-200 ng/mL (10-fold increase in potency as compared to the unmodified protein). All of the acylated forms were more potent than the unmodified protein which had an EC₅₀ of 1000-2000 ng/mL. In addition to the decrease in EC₅₀, the palmitoylated, myristoylated, and lauroylated proteins induced approximately 2-fold more alkaline phosphatase activity than the unmodified protein, while the decanoylated and octanoylated proteins induced approximately 1.5-fold more.

In addition to the increase in potency of the myristoylated form of human Sonic hedgehog observed in the C3H10T1/2 assay, this form is significantly more potent than the unmodified protein at inducing ventral forebrain neurons in explants of embryonic stage E11 rat brain telencephalon. Incubation of E11 telencephalic explants with various concentrations of unmodified, or myristoylated Sonic hedgehog, and subsequent staining of the explants for the products of the dlx and islet-1/2 genes (markers of ventral forebrain neurons), indicates that while induction by the unmodified protein is observed first at 48 nM, induction by the myristyolated form is observed first at 3 nM. Moreover, while the unmodified protein induces restricted expression at 3070 nM, the myristoylated protein induces widespread expression at only 48 nM. A similar increase in potency was observed when explants of embryonic stage E9 presumptive telencephalon were incubated with either the unmodified, or myristoylated proteins. Staining of the explants for the product of the Nkx2.1 gene (an early marker of ventral forebrain neurons), indicated that the unmodified protein induced Nkx2.1 first at 384 nM, while for the myristoylated protein expression of Nkx2.1 was observed first at 12 nM. Moreover, at 48 nM myristoylated Sonic hedgehog, expression of Nkx2.1 was widespread while it was undetectable at this concentration using the unmodified form.

Additionally, myristoylated human Sonic hedgehog has been shown to be significantly more protective than the unmodified protein in reducing the lesion volume which results from administration of malonate into the striatum of the rat brain (See Example 16).

EXAMPLE 9 Chemical Derivatives of the N-terminal Cysteine of Human Sonic Hedgehog

A. General Methods

Alkylation of Proteins. Samples containing about 20 μg of the protein in 50 μL of 6 M guanidine hydrochloride, 50 mM Na₂HPO₄ pH 7.0, were treated with 0.5 μL of 4-vinylpyridine for 2 h at room temperature. The S-pyridylethylated protein was precipitated by addition of 40 volumes of cooled ethanol. The solution was stored at −20° C. for 1 h and then centrifuged at 14,000×g for 8 min at 4° C. The supernatants were discarded and the precipitate was washed with cooled ethanol. The protein was stored at −20° C.

Peptide Mapping. Alkylated protein (0.4 mg/mL in 1 M guanidine hydrochloride, 20 mM Na₂HPO₄ pH 6.0) was digested with endo Lys-C (Wako Pure Chemical Industries, Ltd.) at a 1:20 ratio. The digestion was conducted at room temperature for 30 h. The reaction was stopped by acidification with 5 μL of 25% trifluoroacetic acid. The digest was analyzed on a Waters 2690 Separation Module with a Model 996 photodiode array detector. Prior to injection, solid guanidine hydrochloride was added into the digest to a concentration of 6 M to dissolve insoluble material. A reverse phase Vydac C₁₈ (2.1 mm internal diameter×250 mm) column was used for separation, with a 90 min gradient of 0.1% trifluoroacetic acid/acetonitrile and 0.1% trifluoroacetic acid/acetonitrile at a flow rate of 0.2 mL/min. Individual peaks were collected manually for mass analysis.

Mass Determination. The molecular masses of intact proteins were determined by electrospray ionization mass spectroscopy (ESI-MS) on a Micromass Quattro II triple quadrupole mass spectrometer. Samples were desalted using an on-line Michrom Ultrafast Microprotein Analyzer system with a Reliasil C₄ (1 mm internal diameter×50 mm) column. The flow rate was 20 μL/min. All electrospray mass spectral data were processed using the Micromass MassLynx data system. The molecular masses of peptides were determined by matrix assisted laser desorption ionization time-of-fight mass spectrometry (MALDI-TOF-MS) on a Voyager-DE™ STR (PerSeptive Biosystems, Framingham, Mass.). Sequencing of the modifed peptide was performed by Post-source decay (PSD) measurement on the same instrument. α-Cyano-4-hydroxycinnamic acid was used as the matrix.

N-terminal Sequencing. Proteins were sequenced by Edman degradation on a Perkin-Elmer Applied Biosystems model 477A Pulsed-Liquid Protein Sequencer. PTH-thiaproline was made on line by directly loading thiaproline (thiazolidine-4-carboxylic acid) into the sample loading cartridge of the sequencer.

Bacterial expression and purification of wild type soluble human Sonic hedgehog N-terminal fragment used for chemical modification. Bacterial pellets from cells expressing Shh at 4-5% of the total protein were thawed, resuspended in lysis buffer (25 mM Na₂HPO₄ pH 8, 150 mM NaCl, 1 mM EDTA, 1 mM PMSF, 0.5 mM DTT) at a ratio of 1:4 (w/v) and lysed by two passes through a Gaulin press (mfg. by APV Rannie, Copenhagen, Denmark) at 12,000 p.s.i. All subsequent purification steps were performed at 2-8° C. unless indicated otherwise. The homogenate was centrifuged at 19,000×g for 60 min and MES 0.5 M pH 5, was added to the resulting lysate at a ratio of 1:10 (v/v). The lysate (at pH 5.5) was loaded onto an SP Sepharose Fast Flow (Pharmacia, Piscataway, N.J.) column (4 g E. coli wet weight/mL resin) equilibrated with 25 mM Na₂HPO₄ pH 5.5, 150 mM NaCl. The column was washed with 4 column volumes (CV) of equilibration buffer, then with 3 CV of 25 mM Na₂HPO₄ pH 5.5, 200 mM NaCl, 0.5 mM DTT, and Histag-Shh was eluted with 800 mM NaCl in the same buffer. Elution fractions were analyzed for absorbance at 280 nm and by SDS-PAGE. Imidazole (1M stock solution at pH 7) and NaCl (5 M stock solution) were added to a pool of the peak Shh containing fractions from the SP Sepharose eluate to give final concentrations of 20 mM and 1 M respectively, and this material was loaded onto a NTA-Ni agarose (Qiagen, Santa Clara, Calif.) column (20 mg/mL resin) equilibrated with mM Na₂HPO₄ pH 8, 1 M NaCl, 20 mM imidazole, 0.5 mM DTT. The column was washed with 5 CV of the same buffer and Histag-Shh eluted with 3 CV 25 mM Na₂HPO₄ pH 8, 1 M NaCl, 200 mM imidazole, 0.5 mM DTT. The protein content in the eluate pool from the NTA-Ni column was determined by absorbance at 280 nm. The pool was warmed to room temperature and an equal volume of 2.5 M sodium sulfate was added. The Phenyl Sepharose step was performed at room temperature. The material was loaded onto a Phenyl Sepharose Fast Flow (Pharmacia, Piscataway, N.J.) column (20 mg/mL resin) equilibrated in 25 mM Na₂HPO₄ pH 8, 400 mM NaCl, 1.25 M sodium sulfate, 0.5 mM DTT. Histag-Shh was eluted with 25 mM Na₂HPO₄ pH 8, 400 mM NaCl, 0.5 mM DTT. Typically, we recovered 2-3 g of His-tagged Shh from 0.5 kg of bacterial paste (wet weight). The product was filtered through 0.2 μm filter, aliquoted, and stored at −70° C. The His-tagged Shh was about 95% pure as determined by SDS-PAGE. As a further assessment of the characteristics of the purified product, samples were subjected to evaluation by electrospray ionization mass spectrometry (ESI-MS). Approximately 50% of the protein was missing the N-terminal methionine.

To cleave off the hexahistidine tag, enterokinase (Biozyme, San Diego, Calif.) was incubated with the Histag-Shh at an enzyme: Shh ratio of 1:1000 (w/w) for 2 h at 28° C. Uncleaved Histag-Shh and free Histag were removed by passing the digest through a second NTA-Ni agarose column (20 mg Shh/mL resin). Prior to loading, imidazole (1 M stock solution at pH 7) and NaCl (5M stock solution) were added to the digest to give final concentrations of 20 mM and 600 mM, respectively. This material was loaded onto a NTA-Ni column equilibrated in 25 mM Na₂HPO₄ pH 8, 600 mM NaCl, 20 mM imidazole, 0.5 mM DTT and the flow through collected. The column was washed with 1 CV of the same buffer and pooled with the flow through. MES (0.5 M stock solution at pH 5) was added to the NTA-Ni agarose unbound fraction to a final concentration of 50 mM and two volumes of water were added. This material was loaded onto a second SP Sepharose Fast Flow column (20 mg/mL resin) equilibrated with 5 mM Na₂HPO₄ pH 5.5, 150 mM NaCl, 0.5 mM DTT. The column was washed with 3 CV of equilibration buffer and 1 CV of the same buffer containing 300 mM NaCl. Shh was eluted with 5 mM Na₂HPO₄ pH 5.5, 800 mM NaCl, 0.5 mM DTT. Atomic absorption data revealed that Shh at this stage contained 0.5 mol equivalent of Zn²⁺ . An equimolar concentration of ZnCl₂ was added to the Shh eluant and the protein dialyzed against 5 mM Na₂HPO₄ pH 5.5, 150 mM NaCl, 0.5 mM DTT. The resulting Shh was >98% pure as characterized by SDS-PAGE, size exclusion chromatography (SEC), and ESI-MS and, by atomic absorption, contained between 0.9 and 1.1 Zn²⁺ /Shh.

ESI-MS data for Histag Shh and products resulting after removal of the histag are summarized in Table 7.

TABLE 7 Characterization of Shh by ESI-MS. Mass (Da) Protein Calculated Measured Histag-Shh (-Met) 21433.82 21434 (Intact) 21565.01 21565 Enterokinase-cleaved Shh 19560.02 19560

B. Specific Chemical Modifications

Modification of human Sonic hedgehog with N-ethylmaleimide. Purified Shh in 5 mM Na₂HPO₄ pH 5.5, 150 mM NaCl, 0.5 mM DTT was treated with 10 mM N-ethylmaleimide for 1 h on ice and then dialyzed into 5 mM Na₂HPO₄ pH 5.5, 150 mM NaCl. The MALDI-TOF-MS data showed that the N-ethylmaleimide (NEM)-modified protein had an increase in mass of 126 Da, which indicates that only one cysteine residue in Shh was modified by the reagent. N-terminal sequencing data showed that the protein is sequencible and that an unusual peak, probably PTH-NEM-Cys related, was detected at the first cycle (data not shown). Mass spectrometric analysis of the pyridylethylated-NEM-Shh under denaturing conditions showed that only two cysteine residues in the protein were alkylated, confirming that only the thiol group of the N-terminal cysteine residue was modified by NEM under native conditions (Table 8). The other two cysteine residues, which are apparently buried in the hydrophobic core of the protein, cannot be modified without prior denaturation.

TABLE 8 Characterization of NEM-modified Shh by MS. Protein Mass (Calculated) Mass (Measured) Pyridylethylated NEM Shh 19895 Da if containing 2 free Cys residues 19895 Da if containing 3 free Cys residues 20000 Da

When tested in the C3H10T1/2 assay (See Example 3) the N-ethylmaleimide-modified S hedgehog protein was equal in activity to the unmodified protein. This demonstrates that a free sulfhydryl at the N-terminus of hedgehog is not required for activity and that the N-ethylmaleimide moiety is hydrophobic enough to confer some activity on hedgehog compared to other more hydrophilic modifications, such as conversion of Cys-1 to His or Asp, which produce a reduction in activity.

Modification of human Sonic hedgehog with formaldehyde to form an N-terminal thiaproline, and with acetaldehyde and butyraldehyde to form N-terminal thiaproline derivatives. For formaldehyde modification, purified Shh at 3 mg/mL in 5 mM Na₂HPO₄ pH 5.5, 150 mM NaCl, 0.5 mM DTT was treated with 0.1% formaldehyde, with or without 10% methanol, at room temperature for 1 to 6 h. The protein was either dialyzed against 5 mM Na₂HPO₄ pH 5.5, 150 mM NaCl, or was purified on a CM-Poros column (Perseptive Biosystems) as described below and then dilayzed against 5 mM Na₂HPO₄ pH 5.5, 150 mM NaCl. For modification with acetaldehyde or butyraldehyde, purified Shh at 3 mg/mL in 5 mM Na₂HPO₄ pH 5.5, 150 mM NaCl, 0.5 mM DTT was treated with 0.1% acetaldehyde or butyraldehyde at room temperature for 1 h and then the protein purified on a CM-Poros column. ESI-MS data for the formaldehyde, acetaldehyde-, and butyraldehyde-treated forms of the protein indicated that their masses were 13 Da, 27 Da, and 54 Da higher, respectively, than the unmodified protein (Table 9).

TABLE 9 Expected and observed masses of human Sonic hedgehog treated with formaldehyde, acetaldehyde, and butyraldehyde. Expected Protein mass* (MH⁺) Observed mass* (MH⁺) Unmodified 19560.02 19560 Formaldehyde-treated 19572.03 19573 Acetaldehyde-treated 19586.06 19587 Butyraldehyde-treated 19614.11 19614 *Average masses were used in calculating the expected masses

For the formaldehyde-treated protein, peptide mapping, as described above, demonstrated that the site of the modification occurred in the peptide spanning the first 9 N-terminal residues, and that the exact mass increase was 12 Da. The results of MALDI-PSD MS studies of this peptide indicated that the modification occurred on Cys-1, and could be explained by a modification of the N-terminal α-amine and the thiol side chain of Cys-1 to form a thiaproline (See FIG. 12). The structure of the thiaproline was confirmed by automated N-terminal Edman sequencing using “on-line” prepared PTH-thiaproline as a standard. For the acetaldehyde- and butyraldehyde-treated proteins, the ESI-MS data were consistent with the modifications occuring by means of the same chemistry as for the reaction with formaldehyde, although the exact site of modification has not been established. When tested in the C3H10T1/2 cell-based assay, the formaldehyde-, acetaldehyde-, and butyraldehyde-modified proteins were approximately 8-fold, 2-fold, and 3-fold, respectively, more potent than unmodified Shh.

Modification of human Sonic hedgehog with N-isopropyliodoacetamide. This example shows that modification of human Shh with a hydrophobic derivative of iodoacetamide can enhance the potency of the protein as compared to the unmodified Shh. Purified Shh (1 mg/mL in 5 mM Na₂HPO₄ pH 7.0, 150 mM NaCl, 0.1 mM DTT) was incubated with 1 mM N-isopropyliodoacetamide (NIPIA) at 4° C. for 18 h. DTT was then added to 10 mM final concentration and the sample was dialyzed extensively against 5 mM Na₂HPO4 pH 5.5, 150 mM NaCl, 0.5 mM DTT. The sample was purified on SP Sepharose Fast Flow resin and dialyzed further against 5 mM Na₂HPO₄ pH 5.5, 150 mM NaCl, 0.5 mM DTT. ESI-MS data indicated complete conversion to a species with a mass of 19660, corresponding to the predicted mass value (19659) for the singly modified protein. Specific modification of the N-terminal cysteine was confirmed by peptide mapping of proteolytic fragments. When tested in the C3H10T1/2 cell-based assay, the NIPIA-modified human Shh was approximately 2-fold more potent than the unmodified protein. While the modification of the protein resulted in only a modest increase in potency, it is expected that modification of the protein with long chain alkyl iodoacetamide derivatives will result in hydrophobically-modified forms of the protein with much greater increases in potency, possibly akin to the 100-200-fold increase observed for the palmitoylated, myristoylated, and lauroylated Shh proteins (See Example 8).

Modification of human Sonic hedgehog with 1-bromo-2-butanone to form a six-membered hydrophobic ring at the N-terminus. A thiomorpholinyl-(tetrahydrothiazinyl-) derivative of Shh was prepared by incubating human Shh-N (3 mg/mL in 5 mM Na₂HPO₄ pH 5.5, 150 mM NaCl, 0.15 mM DTT) with 11 mM 1-bromo-2-butanone at room temperature for 60 min, followed by reduction with 5 mM NaCNBH₃ at room temperature for 60 min. The reaction product was purified on a CM-Poros column (Perseptive Biosystems) as described below and was dialyzed against 5 mM Na₂HPO₄ pH 5.5, 150 mM NaCl, 0.5 mM DTT. ESI-MS and proteolytic peptide mapping data indicated that the product was a mixture of the expected thiomorpholinyl derivative (calculated mass=19615, observed mass=19615) and two forms of the protein both with 16 additional mass units. One of these forms is presumably the uncyclized keto-thioether intermediate. The mixture was tested in the C3H10T1/2 assay which indicated that it was approximately 5-fold more potent than the unmodified protein.

EXAMPLE 10 Genetically Engineered Mutations of Human Sonic Hedgehog

A. Genetically Engineered Mutations of the N-terminal Cysteine

In this example, we show that specific replacement of the N-terminal cysteine of human Sonic hedgehog (Cys-1) by single and multiple hydrophobic amino acid residues results in increased potency as compared to the wild type protein in the C3H10T1/2 cell-based assay described in Example 3.

Construction of Shh Cys-1 mutants. The 584 bp NcoI-XhoI restriction fragment carrying the His-tagged wild type Shh N-terminal fragment from p6H-SHH was subcloned into the pUC-derived cloning vector pNN05 to construct the plasmid pEAG649. Cys-1 mutants of soluble human Shh were made by unique site elimination mutagenesis of the pEAG649 plasmid template using a Pharmacia kit following the manufacturer's recommended protocol. In designing the mutagenic primers, if a desired mutation did not produce a restriction site change, a silent mutation producing a restriction site change was introduced into an adjacent codon to facilitate identification of mutant clones following mutagenesis. To avoid aberrant codon usage, substituted codons were selected from those occurring at least once elsewhere in the human Shh cDNA sequence. The following mutagenic primers were used: (1) for C1F: 5′ GGC GAT GAC GAT GAC AAA TTC GGA CCG GGC AGG GGG TTC 3′ (SEQ ID NO:), which introduces an ApoI site to make pEAG837; (2) for C1I: 5′ GGC GAT GAC GAT GAC AAA ATA GGA CCG GGC AGG GGG TTC 3′ (SEQ ID NO:), which loses an RsrII site to make pEAG838; and (3) for C1M: 5′ GGC GAT GAC GAT GAC AAA ATG GGC CCG GGC AGG GGG TTC GGG 3′ (SEQ ID NO:), which loses both RsrII and AvaII sites to make pEAG839. Mutations were confirmed by DNA sequencing through a 180 bp NcoI-BglII restriction fragment carrying the mutant SHH proteins' N-termini in plasmids pEAG837-839. Expression vectors were constructed by subcloning each mutant plasmid's 180 bp NcoI-BglII fragment and the 404 bp BglII-XhoI fragment from pEAG649 into the phosphatase-treated 5.64 kb XhoI-NcoI pET11d vector backbone of p6H-SHH. Presence of the introduced restriction site change was reconfirmed in the expression vector for each Cys-1 mutant (C1F in pEAG840, C1I in pEAG841, and C1M in pEAG842). Expression vectors were transformed into competent E. coli BL21(DE3)pLysS (Stratagene) following the manufacturer's recommended protocol and selected on LB agar plates containing 100 μg/ml ampicillin and 30 μg/mL chloramphenicol. Individual colonies were selected and transformed bacteria were grown to an A₆₀₀ of 0.4-0.6 and induced for 3 h with 0.5 mM IPTG. Bacterial pellets were analyzed for expression of the mutant proteins by reducing SDS-PAGE and by Western blotting.

A soluble human Shh mutant with multiple N-terminal hydrophobic substitutions (C1II) was made by unique site elimination mutagenesis using a Pharmacia kit following the manufacturer's recommended protocol. In designing the mutagenic primers, if a desired mutation did not produce a restriction site change, a silent mutation producing a restriction site change was introduced into an adjacent codon to facilitate identification of mutant clones following mutagenesis. To avoid aberrant codon usage, substituted codons were selected from those occurring at least once elsewhere in the human Shh cDNA sequence. The following mutagenic primer was used on the C1F template plasmid pEAG837 for C1II: 5′ GCG GCG ATG ACG ATG ACA AAA TCA TCG GAC CGG GCA GGG GGT TCG GG 3′ (SEQ ID NO:), which removes an ApoI site to make pEAG872. Mutations were confirmed by DNA sequencing through a 0.59 kb NcoI-XhoI restriction fragment carrying the mutant C1II Shh. An expression vector was constructed by subcloning the mutant plasmid's NcoI-XhoI fragment into the phosphatase-treated 5.64 kb XhoI-NcoI pET11d vector backbone of p6H-SHH. Presence of the introduced restriction site change was reconfirmed in the expression vector for the C1II mutant, pEAG875. The expression vector was transformed into competent E. coli BL21(DE3)pLysS (Stratagene) following the manufacturer's recommended protocol and selected on LB agar plates containing 100 μg/mL ampicillin and 30 μg/mL chloramphenicol. Individual colonies were selected and transformed bacteria were grown to an A₆₀₀ of 0.4-0.6 and induced for 3 h with 0.5 mM IPTG. Bacterial pellets were analyzed as described above to confirm expression of mutant Shh protein.

Purification of Cys-1 mutants of human Sonic hedgehog. The His-tagged mutant hedgehog proteins were purified from the bacterial pellets as described for the wild type protein above except for two modifications. (1) The Phenyl Sepharose step was eliminated and instead the protein pool from the first NTA-Ni agarose column was dialyzed into 25 mM Na₂HPO₄ pH 8, 400 mM NaCl, 0.5 mM DTT in preparation for the enterokinase cleavage step. (2) The final ion exchange step was changed from step elution on SP-Sepharose Fast Flow to gradient elution from a CM-Poros column (Perseptive Biosystems). This was carried out in 50 mM Na₂HPO₄ pH 6.0 with a 0-800 mM NaCl gradient over 30 column volumes. The pooled peak fractions from this step were dialyzed into 5 mM Na₂HPO₄ pH 5.5, 150 mM NaCl and were stored at −80° C. Mass spectrometry of the purified proteins gave the predicted mass ions for each purified form.

Activity of the Cys-1 mutants of human Sonic hedgehog. As shown in Table 10, mutation of the N-terminal cysteine has a significant effect on the potency of the resulting hedgehog protein in the C3H10T1/2 assay. For single changes, potency generally correlates with the hydrophobicity of the substituted amino acid, that is phenylalanine and isoleucine give the greatest activation, methionine is less activating, while histidine and aspartic acid diminish activity compared to the wild type cysteine. Replacing the cysteine with two isoleucines gives an additional increase in activity over the single isoleucine substitution. Given that nine amino acids are categorized as more hydrophobic than cysteine (Proteins: structures and molecular properties, 2^(nd) ed, 1993, T. E. Creighton, W. H. Freeman Co. page 154), the substitutions tested above are clearly not an exhaustive survey of the possible mutations at the N-terminus that can give rise to more active forms of hedgehog. However, the results demonstrate that activation is not restricted to a single amino acid structure and that substitution of more than one amino acid can give a further increase in potency. Therefore, one skilled in the art could create forms of hedgehog with other amino acid substitutions at the N-terminus that would be expected to have greater potency than the wild type protein.

TABLE 10 Relative potency of amino acid modifications of human Sonic hedgehog in the C3H1OT1/2 assay. N-TERMINUS RELATIVE POTENCY C (wild type) 1X M 2X F 4X I 4X II 10X

B. Genetically Engineered Mutations of Internal Residues

Construction of the C1II/A169C mutant. The soluble human Shh mutant C1II/A169C (with cysteine substituted for the dispensable C-terminal residue A169 which is predicted to have a high fractional solvent accessibility) was made by unique site elimination mutagenesis using a Pharmacia kit following the manufacturer's recommended protocol and employing the mutagenic oligo design principles described above. The following mutagenic primer 5′ GAG TCA TCA GCC TCC CGA TTT TGC GCA CAC CGA GTT CTC TGC TTT CAC C 3′ (SEQ ID NO:) was used on C1II Shh template pEAG872 to add an FspI site to make pSYS049. The C1II/A169C mutations were confirmed by DNA sequencing through a 0.59 kb NcoI-XhoI restriction fragment. The expression vector pSYS050 was constructed by subcloning the NcoI-XhoI fragment into the phosphatase-treated 5.64 kb XhoI-NcoI pET11d vector backbone of p6H-SHH. Presence of the introduced restriction site change was reconfirmed in the expression vector. The expression vector was transformed into competent E. coli BL21(DE3)pLysS, colonies were selected, induced, and screened for Shh expression as described above.

Purification of the C1II/A169C mutant. The C1II/A169C mutant was purified as described in Example 9 for wild type Shh except with the following modifications. (1) EDTA was left out of the lysis buffer, (2) the order of the NTA-Ni and SP Sepharose steps were switched and the Phenyl Sepharose step was omitted, (3) after clarification of the lysed bacteria by centrifugation, additional NaCl was added to the supernatant to a final concentration of 300 mM, (4) the elution buffer from the NTA-Ni column contained 25 mM Na₂HPO₄ pH 8.0, 200 mM imidazole, 400 mM NaCl, (5) the elution pool from the NTA-Ni column was diluted with 3 volumes of 100 mM MES pH 5.0 prior to loading onto the SP Sepharose column, (6) prior to addition of enterokinase, the SP Sepharose elution pool was diluted with half a volume of 50 mM Na₂HPO₄ pH 8.0, and (7) the DTT in the elution buffer from the final SP Sepharose column contained 0.2 mM DTT and the elution pool from this step was aliquoted and stored at −70° C.

Hydrophobic modification and activity of the C1II/A169C mutant. For modification with N-(1-pyrene) maleimide (Sigma), purified C1II/A169C at 4.6 mg/mL in 5 mM Na₂HPO₄ pH 5.5, 800 mM NaCl, 0.2 mM DTT was diluted with an equal volume of 50 mM MES pH 6.5 and to this a twentieth of a volume of pyrene maleimide from a 2.5 mg/mL stock in DMSO was added. The sample was incubated for 1 h at room temperature in the dark. At this time additional DTT was added to 0.5 mM and the sample incubated further for an additional hour at room temperature. The modified protein was tested directly for activity in the C3H10T1/2 assay as described in Example 3. Prior to modification, the specific activity of the protein was EC₅₀=0.22 μg/mL, while after treatment with pyrene maleimide the specific activity was increased to EC₅₀=0.08 μg/ml. Increases in the specific activity of the modified product by up to 3-fold were observed frequently indicating that the addition of the hydrophobic group near the C-terminus of Shh resulted in a further increase in activity as compared to the C1II starting material. When compared to the wild type unmodified Sonic hedgehog protein, the N-(1-pyrene) maleimide-modified C1II protein was approximately 30-fold more potent. While pyrene maleimide provided a simple test system for evaluating modification at this site, other hydrophic maleimides or other cysteine targeted chemistries can also be used.

EXAMPLE 11 Comparison of the Potency of Various Hydrophobically-Modified Forms of Human Sonic Hedgehog in the C3H10T1/2 Assay

The activity of various hydrophobically-modified forms of human Sonic he dgehog (prepared using the chemistries and genetic engineeering methods described in Section V) was tested in the C3H10T1/2 assay as described in Example 3.

The derivatives were assayed over a concentration range as described in Example 3. The concentration of hedgehog derivative that resulted in 50% of the maximum response in the assay was compared to the wild type concentration. The relative activities are shown in Table 11, below, and in FIG. 13.

TABLE 11 Relative Potency of Hedgehog Derivatives in the C3H10T1/2 assay. Modification EC₅₀ (x-fold more potent than wild type Shh) C:16 palmitoyl 100 C:14 myristoyl 100 C:12 lauroyl 100 C:10 decanoyl 33 Isoleucyl-isoleucyl 30 with A169C pyrenyl C:8 octanoyl 10 Isoleucyl-isoleucyl 10 C:0 thiaprolyl 8 Thiomorpholinyl 5 Phenylalanyl 4 Isoleucyl 4 N-isopropylacetamidyl 2 Methionyl 2 N-ethylmaleimidyl 1 Cysteinyl (wild type) 1 Aspartyl <1 Histidyl <1

The C3H10T1/2 assay demonstrates that a wide variety of hydrophobic modifications to hedgehog increase the protein's activity when compared to the wild type, unmodified protein. Hydrophilic modifications (aspartic acid and histidine) do not have this effect.

EXAMPLE 12 Evaluating the Efficacy of Hydrophobically-Modified Human Sonic Hedgehog in a Rat Malonate-Induced Striatal Lesion Assay

Injection of malonate, an inhibitor of the mitochondrial enzyme succinate dehydrogenase, into the rat striatum (the rodent equivalent of the primate caudate and putamen) causes degeneration of striatal medium spiny neurons. In humans, degeneration of medium spiny neurons in the caudate and putamen is the primary pathological feature of Huntington's disease. Thus, the malonate-induced striatal lesion in rats can be used as a model to test whether human hedgehog proteins can prevent the death of the neurons that degenerate in Huntington's disease.

Sprague-Dawley rats are injected with various concentrations of hedgehog protein in the striatum using stereotaxic techniques. Stereotaxic injections (2 il) are done under sodium pentobarbital anesthesia (40 mg/kg) and placed at the following coordinates: 0.7 mm anterior to bregma, 2.8 mm lateral to the midline and 5.5 mm ventral to the surface of the skull at bregma. At various times (usually 48 hr) after injection of hedgehog protein, rats are anesthetized with isoflurane and given a stereotaxic injection of malonate (2 imols in 2 il) at the same coordinates in the striatum. Four days after malonate injection, rats are sacrificed and their brains removed for histological analysis. Coronal sections are cut through the striatum at a thickness of 25 im and stained for cytochrome oxidase activity to distinguish lesioned from unlesioned tissue. The volume of the lesion in the striatum is measured using image analysis.

The effect of sonic hedgehog protein constructs given 48 hours before malonate is shown in FIG. 14A. Unmodified sonic hedgehog protein (Shh), myristoylated Shh, C1II-Shh and octyl maleimide Shh all reduce lesion volume to a similar extent in this model. However, the hydrophobically modified proteins (myristoylated Shh, C1II-Shh and octyl maleimide Shh) show an increase in potency relative to the unmodified sonic hedgehog protein. FIG. 14B shows the time course for the effect of pretreatment with myristoylated Shh (0.5 μg in 2 μl) in the malonate striatal lesion model. A statistically significant reduction in lesion volume is seen when myristoylated Shh is given 2 days before malonate, however myristoylated Shh has a greater effect when given either 3 or 4 days before malonate. There was not a statistically significant reduction in lesion volume when myristoylated Shh was given 1 day, 7 days or immediately (0 days) before malonate.

EXAMPLE 13 N-Octylmaleimide derivitization of sHH-N

For a 1 mg/ml Final Concentration

1) Make a 20 mM solution of octylmaleimide (m.w.=209) in DMSO (˜4.2 mg/ml).

2) Dilute stock of 10 mg/ml sHh-N (in 5 mM NaPO4 pH 5.5, 150 mM NaCl, 0.5 mM DTT) 10-fold with PBS (Gibco product #20012-027, pH 7.2) to give a 1 mg/ml (or 50 uM) sHh-N solution. [NOTE: DTT, which competes with sHh-N for maleimide in the subsequent reaction, is also 50 μM in this solution.]

3) Immediately add 1/200 vol. of octylmaleimide to the 1 mg/ml sHh-N (i.e. 5 μl/1 ml). This gives a 2:1 molar ratio (100 μM:50 μM) of octylmaleimide to sHh-N.

4) Mix this solution by gentle inversion of the tube and incubate for 1 hour at room temperature.

5) Finally, 1/1000 vol. of 0.35 M DTT was added to each tube to scavenge any remaining octylmaleimide and to serve as a reductant.

6) For a vehicle control, combine a solution of vehicle (5 mM NaPO4 pH 5.5, 150 mM NaCl, 0.5 mM DTT) with PBS (Gibco product #20012-027, pH 7.2) in a 1:10 ratio. Add 1/400 vol. of 20 mM Octylmaleimide in DMSO and a 1/400 vol. of DMSO to give a final concentration of 50 μM N-octylmaleimide and 0.5% DMSO. Finally, add 1:1000 vol. of 0.35 M DTT.

Approximate Composition of the 1 mg/ml N-octylmaleimide sHh-N Solution

PBS (˜pH 7.2)

50 μM sHh-N conjugated to N-octylmaleimide

50 μM DTT conjugated to N-octylmaleimide

350 μM DTT

0.5% DMSO

Approximate Composition of the N-octylmaleimide Vehicle Solution

PBS (˜pH 7.2)

50 μM DTT conjugated to N-octylmaleimide

350 μM DTT

0.5% DMSO

For a 3 mg/ml Final Concentration

1) Make a 60 mM solution of octylmaleimide (m.w.=209) in DMSO (˜12.6 mg/ml).

2) Dilute stock of 10 mg/ml sHh-N (in 5 mM NaPO4 pH 5.5, 150 mM NaCl, 0.5 mM DTT) 10-fold with PBS (Gibco product #20012-027, pH 7.2) to give a 3 mg/ml (or 150 uM) sHh-N solution. [NOTE: DTT, which competes with sHh-N for maleimide in the subsequent reaction, is also 150 μM in this solution.]

3) Immediately add 1/200 vol. of octylmaleimide to the 3 mg/ml sHh-N (i.e. 5 μl/1 ml). This gives a 2:1 molar ratio (300 μM: 150 μM) of octylmaleimide to sHh-N.

4) Mix this solution by gentle inversion of the tube and incubate for 1 hour at room temperature.

5) Finally, add 1/1000 vol. of 0.35 M DTT to each tube to scavenge any remaining octylmaleimide and to serve as a reductant.

6) For a vehicle control, combine a solution of vehicle (5 mM NaPO4 pH 5.5, 150 mM NaCl, 0.5 mM DTT) with PBS (Gibco product #20012-027, pH 7.2) in a 3:7 ratio. Add 1/400 vol. of 60 mM octylmaleimide in DMSO and a 1/400 vol. of DMSO to give a final concentration of 150 μM N-octylmaleimide and 0.5% DMSO. Finally, add 1:1000 vol. of 0.5 M DTT.

Approximate Composition of the 3 mg/ml N-octylmaleimide sHh-N solution

PBS (˜pH 7.2)

150 μM sHh-N conjugated to N-octylmaleimide

150 μM DTT conjugated to N-octylmaleimide

500 μM DTT

0.5% DMSO

Approximate Composition of the N-octylmaleimide Vehicle Solution

PBS (˜pH 7.2)

150 μM DTT conjugated to N-octylmaleimide

500 μm DTT

0.5% DMSO 0.5% DMSO

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EQUIVALENTS

While we have described a number of embodiments of this invention, it is apparent to persons having ordinary skill in the art that our basic embodiments may be altered to provide other embodiments that utilize the compositions and processes of this invention. Therefore, it will be appreciated that the scope of this invention includes all alternative embodiments and variations which are defined in the foregoing specification and by the claims appended hereto; and the invention is not to be limited by the specific embodiments presented in the examples.

31 1 175 PRT Homo sapiens 1 Cys Gly Pro Gly Arg Val Val Gly Ser Arg Arg Arg Pro Pro Arg Lys 1 5 10 15 Leu Val Pro Leu Ala Tyr Lys Gln Phe Ser Pro Asn Val Pro Glu Lys 20 25 30 Thr Leu Gly Ala Ser Gly Arg Tyr Glu Gly Lys Ile Ala Arg Ser Ser 35 40 45 Glu Arg Phe Lys Glu Leu Thr Pro Asn Tyr Asn Pro Asp Ile Ile Phe 50 55 60 Lys Asp Glu Glu Asn Thr Gly Ala Asp Arg Leu Met Thr Gln Arg Cys 65 70 75 80 Lys Asp Arg Leu Asn Ser Leu Ala Ile Ser Val Met Asn Gln Trp Pro 85 90 95 Gly Val Lys Leu Arg Val Thr Glu Gly Trp Asp Glu Asp Gly His His 100 105 110 Ser Glu Glu Ser Leu His Tyr Glu Gly Arg Ala Val Asp Ile Thr Thr 115 120 125 Ser Asp Arg Asp Arg Asn Lys Tyr Gly Leu Leu Ala Arg Leu Ala Val 130 135 140 Glu Ala Gly Phe Asp Trp Val Tyr Tyr Glu Ser Lys Ala His Val His 145 150 155 160 Cys Ser Val Lys Ser Glu His Ser Ala Ala Ala Lys Thr Gly Gly 165 170 175 2 174 PRT Homo sapiens 2 Cys Gly Pro Gly Arg Gly Phe Gly Lys Arg Arg His Pro Lys Lys Leu 1 5 10 15 Thr Pro Leu Ala Tyr Lys Gln Phe Ile Pro Asn Val Ala Glu Lys Thr 20 25 30 Leu Gly Ala Ser Gly Arg Tyr Glu Gly Lys Ile Ser Arg Asn Ser Glu 35 40 45 Arg Phe Lys Glu Leu Thr Pro Asn Tyr Asn Pro Asp Ile Ile Phe Lys 50 55 60 Asp Glu Glu Asn Thr Gly Ala Asp Arg Leu Met Thr Gln Arg Cys Lys 65 70 75 80 Asp Lys Leu Asn Ala Leu Ala Ile Ser Val Met Asn Gln Trp Pro Gly 85 90 95 Val Lys Leu Arg Val Thr Glu Gly Trp Asp Glu Asp Gly His His Ser 100 105 110 Glu Glu Ser Leu His Tyr Glu Gly Arg Ala Val Asp Ile Thr Thr Ser 115 120 125 Asp Arg Asp Arg Ser Lys Tyr Gly Met Leu Ala Arg Leu Ala Val Glu 130 135 140 Ala Gly Phe Asp Trp Val Tyr Tyr Glu Ser Lys Ala His Ile His Cys 145 150 155 160 Ser Val Lys Ala Glu Asn Ser Val Ala Ala Lys Ser Gly Gly 165 170 3 176 PRT Homo sapiens 3 Cys Gly Pro Gly Arg Gly Pro Val Gly Arg Arg Arg Tyr Ala Arg Lys 1 5 10 15 Gln Leu Val Pro Leu Leu Tyr Lys Gln Phe Val Pro Gly Val Pro Glu 20 25 30 Arg Thr Leu Gly Ala Ser Gly Pro Ala Glu Gly Arg Val Ala Arg Gly 35 40 45 Ser Glu Arg Phe Arg Asp Leu Val Pro Asn Tyr Asn Pro Asp Ile Ile 50 55 60 Phe Lys Asp Glu Glu Asn Ser Gly Ala Asp Arg Leu Met Thr Glu Arg 65 70 75 80 Cys Lys Glu Arg Val Asn Ala Leu Ala Ile Ala Val Met Asn Met Trp 85 90 95 Pro Gly Val Arg Leu Arg Val Thr Glu Gly Trp Asp Glu Asp Gly His 100 105 110 His Ala Gln Asp Ser Leu His Tyr Glu Gly Arg Ala Leu Asp Ile Thr 115 120 125 Thr Ser Asp Arg Asp Arg Asn Lys Tyr Gly Leu Leu Ala Arg Leu Ala 130 135 140 Val Glu Ala Gly Phe Asp Trp Val Tyr Tyr Glu Ser Arg Asn His Val 145 150 155 160 His Val Ser Val Lys Ala Asp Asn Ser Leu Ala Val Arg Ala Gly Gly 165 170 175 4 176 PRT Artificial Sequence Description of Artificial Sequence Consensus sequence 4 Cys Gly Pro Gly Arg Xaa Xaa Xaa Xaa Xaa Arg Arg Xaa Xaa Xaa Lys 1 5 10 15 Xaa Leu Xaa Pro Leu Xaa Tyr Lys Gln Phe Xaa Pro Xaa Val Xaa Glu 20 25 30 Lys Thr Leu Gly Ala Ser Gly Arg Xaa Glu Gly Lys Xaa Xaa Arg Xaa 35 40 45 Ser Glu Arg Phe Lys Xaa Leu Xaa Pro Asn Tyr Asn Pro Asp Ile Ile 50 55 60 Phe Lys Asp Glu Glu Asn Xaa Gly Ala Asp Arg Leu Met Thr Xaa Arg 65 70 75 80 Cys Lys Xaa Xaa Xaa Asn Ser Leu Ala Ile Xaa Val Met Asn Xaa Trp 85 90 95 Pro Gly Val Lys Leu Arg Val Thr Glu Gly Trp Asp Glu Asp Gly His 100 105 110 His Xaa Xaa Xaa Ser Leu His Tyr Glu Gly Arg Ala Val Asp Ile Thr 115 120 125 Thr Ser Asp Arg Asp Arg Xaa Lys Tyr Gly Xaa Leu Ala Arg Leu Ala 130 135 140 Val Glu Ala Gly Phe Asp Trp Val Tyr Tyr Glu Ser Xaa Xaa His Xaa 145 150 155 160 His Xaa Ser Val Lys Xaa Xaa Xaa Ser Xaa Ala Ala Xaa Xaa Gly Gly 165 170 175 5 1277 DNA Gallus sp. CDS (1)..(1275) 5 atg gtc gaa atg ctg ctg ttg aca aga att ctc ttg gtg ggc ttc atc 48 Met Val Glu Met Leu Leu Leu Thr Arg Ile Leu Leu Val Gly Phe Ile 1 5 10 15 tgc gct ctt tta gtc tcc tct ggg ctg act tgt gga cca ggc agg ggc 96 Cys Ala Leu Leu Val Ser Ser Gly Leu Thr Cys Gly Pro Gly Arg Gly 20 25 30 att gga aaa agg agg cac ccc aaa aag ctg acc ccg tta gcc tat aag 144 Ile Gly Lys Arg Arg His Pro Lys Lys Leu Thr Pro Leu Ala Tyr Lys 35 40 45 cag ttt att ccc aat gtg gca gag aag acc cta ggg gcc agt gga aga 192 Gln Phe Ile Pro Asn Val Ala Glu Lys Thr Leu Gly Ala Ser Gly Arg 50 55 60 tat gaa ggg aag atc aca aga aac tcc gag aga ttt aaa gaa cta acc 240 Tyr Glu Gly Lys Ile Thr Arg Asn Ser Glu Arg Phe Lys Glu Leu Thr 65 70 75 80 cca aat tac aac cct gac att att ttt aag gat gaa gag aac acg gga 288 Pro Asn Tyr Asn Pro Asp Ile Ile Phe Lys Asp Glu Glu Asn Thr Gly 85 90 95 gct gac aga ctg atg act cag cgc tgc aag gac aag ctg aat gcc ctg 336 Ala Asp Arg Leu Met Thr Gln Arg Cys Lys Asp Lys Leu Asn Ala Leu 100 105 110 gcg atc tcg gtg atg aac cag tgg ccc ggg gtg aag ctg cgg gtg acc 384 Ala Ile Ser Val Met Asn Gln Trp Pro Gly Val Lys Leu Arg Val Thr 115 120 125 gag ggc tgg gac gag gat ggc cat cac tcc gag gaa tcg ctg cac tac 432 Glu Gly Trp Asp Glu Asp Gly His His Ser Glu Glu Ser Leu His Tyr 130 135 140 gag ggt cgc gcc gtg gac atc acc acg tcg gat cgg gac cgc agc aag 480 Glu Gly Arg Ala Val Asp Ile Thr Thr Ser Asp Arg Asp Arg Ser Lys 145 150 155 160 tac gga atg ctg gcc cgc ctc gcc gtc gag gcc ggc ttc gac tgg gtc 528 Tyr Gly Met Leu Ala Arg Leu Ala Val Glu Ala Gly Phe Asp Trp Val 165 170 175 tac tac gag tcc aag gcg cac atc cac tgc tcc gtc aaa gca gaa aac 576 Tyr Tyr Glu Ser Lys Ala His Ile His Cys Ser Val Lys Ala Glu Asn 180 185 190 tca gtg gca gcg aaa tca gga ggc tgc ttc cct ggc tca gcc aca gtg 624 Ser Val Ala Ala Lys Ser Gly Gly Cys Phe Pro Gly Ser Ala Thr Val 195 200 205 cac ctg gag cat gga ggc acc aag ctg gtg aag gac ctg agc cct ggg 672 His Leu Glu His Gly Gly Thr Lys Leu Val Lys Asp Leu Ser Pro Gly 210 215 220 gac cgc gtg ctg gct gct gac gcg gac ggc cgg ctg ctc tac agt gac 720 Asp Arg Val Leu Ala Ala Asp Ala Asp Gly Arg Leu Leu Tyr Ser Asp 225 230 235 240 ttc ctc acc ttc ctc gac cgg atg gac agc tcc cga aag ctc ttc tac 768 Phe Leu Thr Phe Leu Asp Arg Met Asp Ser Ser Arg Lys Leu Phe Tyr 245 250 255 gtc atc gag acg cgg cag ccc cgg gcc cgg ctg cta ctg acg gcg gcc 816 Val Ile Glu Thr Arg Gln Pro Arg Ala Arg Leu Leu Leu Thr Ala Ala 260 265 270 cac ctg ctc ttt gtg gcc ccc cag cac aac cag tcg gag gcc aca ggg 864 His Leu Leu Phe Val Ala Pro Gln His Asn Gln Ser Glu Ala Thr Gly 275 280 285 tcc acc agt ggc cag gcg ctc ttc gcc agc aac gtg aag cct ggc caa 912 Ser Thr Ser Gly Gln Ala Leu Phe Ala Ser Asn Val Lys Pro Gly Gln 290 295 300 cgt gtc tat gtg ctg ggc gag ggc ggg cag cag ctg ctg ccg gcg tct 960 Arg Val Tyr Val Leu Gly Glu Gly Gly Gln Gln Leu Leu Pro Ala Ser 305 310 315 320 gtc cac agc gtc tca ttg cgg gag gag gcg tcc gga gcc tac gcc cca 1008 Val His Ser Val Ser Leu Arg Glu Glu Ala Ser Gly Ala Tyr Ala Pro 325 330 335 ctc acc gcc cag ggc acc atc ctc atc aac cgg gtg ttg gcc tcc tgc 1056 Leu Thr Ala Gln Gly Thr Ile Leu Ile Asn Arg Val Leu Ala Ser Cys 340 345 350 tac gcc gtc atc gag gag cac agt tgg gcc cat tgg gcc ttc gca cca 1104 Tyr Ala Val Ile Glu Glu His Ser Trp Ala His Trp Ala Phe Ala Pro 355 360 365 ttc cgc ttg gct cag ggg ctg ctg gcc gcc ctc tgc cca gat ggg gcc 1152 Phe Arg Leu Ala Gln Gly Leu Leu Ala Ala Leu Cys Pro Asp Gly Ala 370 375 380 atc cct act gcc gcc acc acc acc act ggc atc cat tgg tac tca cgg 1200 Ile Pro Thr Ala Ala Thr Thr Thr Thr Gly Ile His Trp Tyr Ser Arg 385 390 395 400 ctc ctc tac cgc atc ggc agc tgg gtg ctg gat ggt gac gcg ctg cat 1248 Leu Leu Tyr Arg Ile Gly Ser Trp Val Leu Asp Gly Asp Ala Leu His 405 410 415 ccg ctg ggc atg gtg gca ccg gcc agc tg 1277 Pro Leu Gly Met Val Ala Pro Ala Ser 420 425 6 1190 DNA Murine sp. CDS (1)..(1188) 6 atg gct ctg ccg gcc agt ctg ttg ccc ctg tgc tgc ttg gca ctc ttg 48 Met Ala Leu Pro Ala Ser Leu Leu Pro Leu Cys Cys Leu Ala Leu Leu 1 5 10 15 gca cta tct gcc cag agc tgc ggg ccg ggc cga gga ccg gtt ggc cgg 96 Ala Leu Ser Ala Gln Ser Cys Gly Pro Gly Arg Gly Pro Val Gly Arg 20 25 30 cgg cgt tat gtg cgc aag caa ctt gtg cct ctg cta tac aag cag ttt 144 Arg Arg Tyr Val Arg Lys Gln Leu Val Pro Leu Leu Tyr Lys Gln Phe 35 40 45 gtg ccc agt atg ccc gag cgg acc ctg ggc gcg agt ggg cca gcg gag 192 Val Pro Ser Met Pro Glu Arg Thr Leu Gly Ala Ser Gly Pro Ala Glu 50 55 60 ggg agg gta aca agg ggg tcg gag cgc ttc cgg gac ctc gta ccc aac 240 Gly Arg Val Thr Arg Gly Ser Glu Arg Phe Arg Asp Leu Val Pro Asn 65 70 75 80 tac aac ccc gac ata atc ttc aag gat gag gag aac agc ggc gca gac 288 Tyr Asn Pro Asp Ile Ile Phe Lys Asp Glu Glu Asn Ser Gly Ala Asp 85 90 95 cgc ctg atg aca gag cgt tgc aaa gag cgg gtg aac gct cta gcc atc 336 Arg Leu Met Thr Glu Arg Cys Lys Glu Arg Val Asn Ala Leu Ala Ile 100 105 110 gcg gtg atg aac atg tgg ccc gga gta cgc cta cgt gtg act gaa ggc 384 Ala Val Met Asn Met Trp Pro Gly Val Arg Leu Arg Val Thr Glu Gly 115 120 125 tgg gac gag gac ggc cac cac gca cag gat tca ctc cac tac gaa ggc 432 Trp Asp Glu Asp Gly His His Ala Gln Asp Ser Leu His Tyr Glu Gly 130 135 140 cgt gcc ttg gac atc acc acg tct gac cgt gac cgt aat aag tat ggt 480 Arg Ala Leu Asp Ile Thr Thr Ser Asp Arg Asp Arg Asn Lys Tyr Gly 145 150 155 160 ttg ttg gcg cgc cta gct gtg gaa gcc gga ttc gac tgg gtc tac tac 528 Leu Leu Ala Arg Leu Ala Val Glu Ala Gly Phe Asp Trp Val Tyr Tyr 165 170 175 gag tcc cgc aac cac atc cac gta tcg gtc aaa gct gat aac tca ctg 576 Glu Ser Arg Asn His Ile His Val Ser Val Lys Ala Asp Asn Ser Leu 180 185 190 gcg gtc cga gcc gga ggc tgc ttt ccg gga aat gcc acg gtg cgc ttg 624 Ala Val Arg Ala Gly Gly Cys Phe Pro Gly Asn Ala Thr Val Arg Leu 195 200 205 cgg agc ggc gaa cgg aag ggg ctg agg gaa cta cat cgt ggt gac tgg 672 Arg Ser Gly Glu Arg Lys Gly Leu Arg Glu Leu His Arg Gly Asp Trp 210 215 220 gta ctg gcc gct gat gca gcg ggc cga gtg gta ccc acg cca gtg ctg 720 Val Leu Ala Ala Asp Ala Ala Gly Arg Val Val Pro Thr Pro Val Leu 225 230 235 240 ctc ttc ctg gac cgg gat ctg cag cgc cgc gcc tcg ttc gtg gct gtg 768 Leu Phe Leu Asp Arg Asp Leu Gln Arg Arg Ala Ser Phe Val Ala Val 245 250 255 gag acc gag cgg cct ccg cgc aaa ctg ttg ctc aca ccc tgg cat ctg 816 Glu Thr Glu Arg Pro Pro Arg Lys Leu Leu Leu Thr Pro Trp His Leu 260 265 270 gtg ttc gct gct cgc ggg cca gcg cct gct cca ggt gac ttt gca ccg 864 Val Phe Ala Ala Arg Gly Pro Ala Pro Ala Pro Gly Asp Phe Ala Pro 275 280 285 gtg ttc gcg cgc cgc tta cgt gct ggc gac tcg gtg ctg gct ccc ggc 912 Val Phe Ala Arg Arg Leu Arg Ala Gly Asp Ser Val Leu Ala Pro Gly 290 295 300 ggg gac gcg ctc cag ccg gcg cgc gta gcc cgc gtg gcg cgc gag gaa 960 Gly Asp Ala Leu Gln Pro Ala Arg Val Ala Arg Val Ala Arg Glu Glu 305 310 315 320 gcc gtg ggc gtg ttc gca ccg ctc act gcg cac ggg acg ctg ctg gtc 1008 Ala Val Gly Val Phe Ala Pro Leu Thr Ala His Gly Thr Leu Leu Val 325 330 335 aac gac gtc ctc gcc tcc tgc tac gcg gtt cta gag agt cac cag tgg 1056 Asn Asp Val Leu Ala Ser Cys Tyr Ala Val Leu Glu Ser His Gln Trp 340 345 350 gcc cac cgc gcc ttc gcc cct ttg cgg ctg ctg cac gcg ctc ggg gct 1104 Ala His Arg Ala Phe Ala Pro Leu Arg Leu Leu His Ala Leu Gly Ala 355 360 365 ctg ctc cct ggg ggt gca gtc cag ccg act ggc atg cat tgg tac tct 1152 Leu Leu Pro Gly Gly Ala Val Gln Pro Thr Gly Met His Trp Tyr Ser 370 375 380 cgc ctc ctt tac cgc ttg gcc gag gag tta atg ggc tg 1190 Arg Leu Leu Tyr Arg Leu Ala Glu Glu Leu Met Gly 385 390 395 7 1281 DNA Murine sp. CDS (1)..(1233) 7 atg tct ccc gcc tgg ctc cgg ccc cga ctg cgg ttc tgt ctg ttc ctg 48 Met Ser Pro Ala Trp Leu Arg Pro Arg Leu Arg Phe Cys Leu Phe Leu 1 5 10 15 ctg ctg ctg ctt ctg gtg ccg gcg gcg cgg ggc tgc ggg ccg ggc cgg 96 Leu Leu Leu Leu Leu Val Pro Ala Ala Arg Gly Cys Gly Pro Gly Arg 20 25 30 gtg gtg ggc agc cgc cgg agg ccg cct cgc aag ctc gtg cct ctt gcc 144 Val Val Gly Ser Arg Arg Arg Pro Pro Arg Lys Leu Val Pro Leu Ala 35 40 45 tac aag cag ttc agc ccc aac gtg ccg gag aag acc ctg ggc gcc agc 192 Tyr Lys Gln Phe Ser Pro Asn Val Pro Glu Lys Thr Leu Gly Ala Ser 50 55 60 ggg cgc tac gaa ggc aag atc gcg cgc agc tct gag cgc ttc aaa gag 240 Gly Arg Tyr Glu Gly Lys Ile Ala Arg Ser Ser Glu Arg Phe Lys Glu 65 70 75 80 ctc acc ccc aac tac aat ccc gac atc atc ttc aag gac gag gag aac 288 Leu Thr Pro Asn Tyr Asn Pro Asp Ile Ile Phe Lys Asp Glu Glu Asn 85 90 95 acg ggt gcc gac cgc ctc atg acc cag cgc tgc aag gac cgt ctg aac 336 Thr Gly Ala Asp Arg Leu Met Thr Gln Arg Cys Lys Asp Arg Leu Asn 100 105 110 tca ctg gcc atc tct gtc atg aac cag tgg cct ggt gtg aaa ctg cgg 384 Ser Leu Ala Ile Ser Val Met Asn Gln Trp Pro Gly Val Lys Leu Arg 115 120 125 gtg acc gaa ggc cgg gat gaa gat ggc cat cac tca gag gag tct tta 432 Val Thr Glu Gly Arg Asp Glu Asp Gly His His Ser Glu Glu Ser Leu 130 135 140 cac tat gag ggc cgc gcg gtg gat atc acc acc tca gac cgt gac cga 480 His Tyr Glu Gly Arg Ala Val Asp Ile Thr Thr Ser Asp Arg Asp Arg 145 150 155 160 aat aag tat gga ctg ctg gcg cgc tta gca gtg gag gcc ggc ttc gac 528 Asn Lys Tyr Gly Leu Leu Ala Arg Leu Ala Val Glu Ala Gly Phe Asp 165 170 175 tgg gtg tat tac gag tcc aag gcc cac gtg cat tgc tct gtc aag tct 576 Trp Val Tyr Tyr Glu Ser Lys Ala His Val His Cys Ser Val Lys Ser 180 185 190 gag cat tcg gcc gct gcc aag aca ggt ggc tgc ttt cct gcc gga gcc 624 Glu His Ser Ala Ala Ala Lys Thr Gly Gly Cys Phe Pro Ala Gly Ala 195 200 205 cag gtg cgc cta gag aac ggg gag cgt gtg gcc ctg tca gct gta aag 672 Gln Val Arg Leu Glu Asn Gly Glu Arg Val Ala Leu Ser Ala Val Lys 210 215 220 cca gga gac cgg gtg ctg gcc atg ggg gag gat ggg acc ccc acc ttc 720 Pro Gly Asp Arg Val Leu Ala Met Gly Glu Asp Gly Thr Pro Thr Phe 225 230 235 240 agt gat gtg ctt att ttc ctg gac cgc gag cca aac cgg ctg aga gct 768 Ser Asp Val Leu Ile Phe Leu Asp Arg Glu Pro Asn Arg Leu Arg Ala 245 250 255 ttc cag gtc atc gag act cag gat cct ccg cgt cgg ctg gcg ctc acg 816 Phe Gln Val Ile Glu Thr Gln Asp Pro Pro Arg Arg Leu Ala Leu Thr 260 265 270 cct gcc cac ctg ctc ttc att gcg gac aat cat aca gaa cca gca gcc 864 Pro Ala His Leu Leu Phe Ile Ala Asp Asn His Thr Glu Pro Ala Ala 275 280 285 cac ttc cgg gcc aca ttt gcc agc cat gtg caa cca ggc caa tat gtg 912 His Phe Arg Ala Thr Phe Ala Ser His Val Gln Pro Gly Gln Tyr Val 290 295 300 ctg gta tca ggg gta cca ggc ctc cag cct gct cgg gtg gca gct gtc 960 Leu Val Ser Gly Val Pro Gly Leu Gln Pro Ala Arg Val Ala Ala Val 305 310 315 320 tcc acc cac gtg gcc ctt ggg tcc tat gct cct ctc aca agg cat ggg 1008 Ser Thr His Val Ala Leu Gly Ser Tyr Ala Pro Leu Thr Arg His Gly 325 330 335 aca ctt gtg gtg gag gat gtg gtg gcc tcc tgc ttt gca gct gtg gct 1056 Thr Leu Val Val Glu Asp Val Val Ala Ser Cys Phe Ala Ala Val Ala 340 345 350 gac cac cat ctg gct cag ttg gcc ttc tgg ccc ctg cga ctg ttt ccc 1104 Asp His His Leu Ala Gln Leu Ala Phe Trp Pro Leu Arg Leu Phe Pro 355 360 365 agt ttg gca tgg ggc agc tgg acc cca agt gag ggt gtt cac tcc tac 1152 Ser Leu Ala Trp Gly Ser Trp Thr Pro Ser Glu Gly Val His Ser Tyr 370 375 380 cct cag atg ctc tac cgc ctg ggg cgt ctc ttg cta gaa gag agc acc 1200 Pro Gln Met Leu Tyr Arg Leu Gly Arg Leu Leu Leu Glu Glu Ser Thr 385 390 395 400 ttc cat cca ctg ggc atg tct ggg gca gga agc tgaagggact ctaaccactg 1253 Phe His Pro Leu Gly Met Ser Gly Ala Gly Ser 405 410 ccctcctgga actgctgtgc gtggatcc 1281 8 1313 DNA Murine sp. CDS (1)..(1311) 8 atg ctg ctg ctg ctg gcc aga tgt ttt ctg gtg atc ctt gct tcc tcg 48 Met Leu Leu Leu Leu Ala Arg Cys Phe Leu Val Ile Leu Ala Ser Ser 1 5 10 15 ctg ctg gtg tgc ccc ggg ctg gcc tgt ggg ccc ggc agg ggg ttt gga 96 Leu Leu Val Cys Pro Gly Leu Ala Cys Gly Pro Gly Arg Gly Phe Gly 20 25 30 aag agg cgg cac ccc aaa aag ctg acc cct tta gcc tac aag cag ttt 144 Lys Arg Arg His Pro Lys Lys Leu Thr Pro Leu Ala Tyr Lys Gln Phe 35 40 45 att ccc aac gta gcc gag aag acc cta ggg gcc agc ggc aga tat gaa 192 Ile Pro Asn Val Ala Glu Lys Thr Leu Gly Ala Ser Gly Arg Tyr Glu 50 55 60 ggg aag atc aca aga aac tcc gaa cga ttt aag gaa ctc acc ccc aat 240 Gly Lys Ile Thr Arg Asn Ser Glu Arg Phe Lys Glu Leu Thr Pro Asn 65 70 75 80 tac aac ccc gac atc ata ttt aag gat gag gaa aac acg gga gca gac 288 Tyr Asn Pro Asp Ile Ile Phe Lys Asp Glu Glu Asn Thr Gly Ala Asp 85 90 95 cgg ctg atg act cag agg tgc aaa gac aag tta aat gcc ttg gcc atc 336 Arg Leu Met Thr Gln Arg Cys Lys Asp Lys Leu Asn Ala Leu Ala Ile 100 105 110 tct gtg atg aac cag tgg cct gga gtg agg ctg cga gtg acc gag ggc 384 Ser Val Met Asn Gln Trp Pro Gly Val Arg Leu Arg Val Thr Glu Gly 115 120 125 tgg gat gag gac ggc cat cat tca gag gag tct cta cac tat gag ggt 432 Trp Asp Glu Asp Gly His His Ser Glu Glu Ser Leu His Tyr Glu Gly 130 135 140 cga gca gtg gac atc acc acg tcc gac cgg gac cgc agc aag tac ggc 480 Arg Ala Val Asp Ile Thr Thr Ser Asp Arg Asp Arg Ser Lys Tyr Gly 145 150 155 160 atg ctg gct cgc ctg gct gtg gaa gca ggt ttc gac tgg gtc tac tat 528 Met Leu Ala Arg Leu Ala Val Glu Ala Gly Phe Asp Trp Val Tyr Tyr 165 170 175 gaa tcc aaa gct cac atc cac tgt tct gtg aaa gca gag aac tcc gtg 576 Glu Ser Lys Ala His Ile His Cys Ser Val Lys Ala Glu Asn Ser Val 180 185 190 gcg gcc aaa tcc ggc ggc tgt ttc ccg gga tcc gcc acc gtg cac ctg 624 Ala Ala Lys Ser Gly Gly Cys Phe Pro Gly Ser Ala Thr Val His Leu 195 200 205 gag cag ggc ggc acc aag ctg gtg aag gac tta cgt ccc gga gac cgc 672 Glu Gln Gly Gly Thr Lys Leu Val Lys Asp Leu Arg Pro Gly Asp Arg 210 215 220 gtg ctg gcg gct gac gac cag ggc cgg ctg ctg tac agc gac ttc ctc 720 Val Leu Ala Ala Asp Asp Gln Gly Arg Leu Leu Tyr Ser Asp Phe Leu 225 230 235 240 acc ttc ctg gac cgc gac gaa ggc gcc aag aag gtc ttc tac gtg atc 768 Thr Phe Leu Asp Arg Asp Glu Gly Ala Lys Lys Val Phe Tyr Val Ile 245 250 255 gag acg ctg gag ccg cgc gag cgc ctg ctg ctc acc gcc gcg cac ctg 816 Glu Thr Leu Glu Pro Arg Glu Arg Leu Leu Leu Thr Ala Ala His Leu 260 265 270 ctc ttc gtg gcg ccg cac aac gac tcg ggg ccc acg ccc ggg cca agc 864 Leu Phe Val Ala Pro His Asn Asp Ser Gly Pro Thr Pro Gly Pro Ser 275 280 285 gcg ctc ttt gcc agc cgc gtg cgc ccc ggg cag cgc gtg tac gtg gtg 912 Ala Leu Phe Ala Ser Arg Val Arg Pro Gly Gln Arg Val Tyr Val Val 290 295 300 gct gaa cgc ggc ggg gac cgc cgg ctg ctg ccc gcc gcg gtg cac agc 960 Ala Glu Arg Gly Gly Asp Arg Arg Leu Leu Pro Ala Ala Val His Ser 305 310 315 320 gtg acg ctg cga gag gag gag gcg ggc gcg tac gcg ccg ctc acg gcg 1008 Val Thr Leu Arg Glu Glu Glu Ala Gly Ala Tyr Ala Pro Leu Thr Ala 325 330 335 cac ggc acc att ctc atc aac cgg gtg ctc gcc tcg tgc tac gct gtc 1056 His Gly Thr Ile Leu Ile Asn Arg Val Leu Ala Ser Cys Tyr Ala Val 340 345 350 atc gag gag cac agc tgg gca cac cgg gcc ttc gcg cct ttc cgc ctg 1104 Ile Glu Glu His Ser Trp Ala His Arg Ala Phe Ala Pro Phe Arg Leu 355 360 365 gcg cac gcg ctg ctg gcc gcg ctg gca ccc gcc cgc acg gac ggc ggg 1152 Ala His Ala Leu Leu Ala Ala Leu Ala Pro Ala Arg Thr Asp Gly Gly 370 375 380 ggc ggg ggc agc atc cct gca gcg caa tct gca acg gaa gcg agg ggc 1200 Gly Gly Gly Ser Ile Pro Ala Ala Gln Ser Ala Thr Glu Ala Arg Gly 385 390 395 400 gcg gag ccg act gcg ggc atc cac tgg tac tcg cag ctg ctc tac cac 1248 Ala Glu Pro Thr Ala Gly Ile His Trp Tyr Ser Gln Leu Leu Tyr His 405 410 415 att ggc acc tgg ctg ttg gac agc gag acc atg cat ccc ttg gga atg 1296 Ile Gly Thr Trp Leu Leu Asp Ser Glu Thr Met His Pro Leu Gly Met 420 425 430 gcg gtc aag tcc agc tg 1313 Ala Val Lys Ser Ser 435 9 1256 DNA Brachydanio rerio CDS (1)..(1254) 9 atg cgg ctt ttg acg aga gtg ctg ctg gtg tct ctt ctc act ctg tcc 48 Met Arg Leu Leu Thr Arg Val Leu Leu Val Ser Leu Leu Thr Leu Ser 1 5 10 15 ttg gtg gtg tcc gga ctg gcc tgc ggt cct ggc aga ggc tac ggc aga 96 Leu Val Val Ser Gly Leu Ala Cys Gly Pro Gly Arg Gly Tyr Gly Arg 20 25 30 aga aga cat ccg aag aag ctg aca cct ctc gcc tac aag cag ttc ata 144 Arg Arg His Pro Lys Lys Leu Thr Pro Leu Ala Tyr Lys Gln Phe Ile 35 40 45 cct aat gtc gcg gag aag acc tta ggg gcc agc ggc aga tac gag ggc 192 Pro Asn Val Ala Glu Lys Thr Leu Gly Ala Ser Gly Arg Tyr Glu Gly 50 55 60 aag ata acg cgc aat tcg gag aga ttt aaa gaa ctt act cca aat tac 240 Lys Ile Thr Arg Asn Ser Glu Arg Phe Lys Glu Leu Thr Pro Asn Tyr 65 70 75 80 aat ccc gac att atc ttt aag gat gag gag aac acg gga gcg gac agg 288 Asn Pro Asp Ile Ile Phe Lys Asp Glu Glu Asn Thr Gly Ala Asp Arg 85 90 95 ctc atg aca cag aga tgc aaa gac aag ctg aac tcg ctg gcc atc tct 336 Leu Met Thr Gln Arg Cys Lys Asp Lys Leu Asn Ser Leu Ala Ile Ser 100 105 110 gta atg aac cac tgg cca ggg gtt aag ctg cgt gtg aca gag ggc tgg 384 Val Met Asn His Trp Pro Gly Val Lys Leu Arg Val Thr Glu Gly Trp 115 120 125 gat gag gac ggt cac cat ttt gaa gaa tca ctc cac tac gag gga aga 432 Asp Glu Asp Gly His His Phe Glu Glu Ser Leu His Tyr Glu Gly Arg 130 135 140 gct gtt gat att acc acc tct gac cga gac aag agc aaa tac ggg aca 480 Ala Val Asp Ile Thr Thr Ser Asp Arg Asp Lys Ser Lys Tyr Gly Thr 145 150 155 160 ctg tct cgc cta gct gtg gag gct gga ttt gac tgg gtc tat tac gag 528 Leu Ser Arg Leu Ala Val Glu Ala Gly Phe Asp Trp Val Tyr Tyr Glu 165 170 175 tcc aaa gcc cac att cat tgc tct gtc aaa gca gaa aat tcg gtt gct 576 Ser Lys Ala His Ile His Cys Ser Val Lys Ala Glu Asn Ser Val Ala 180 185 190 gcg aaa tct ggg ggc tgt ttc cca ggt tcg gct ctg gtc tcg ctc cag 624 Ala Lys Ser Gly Gly Cys Phe Pro Gly Ser Ala Leu Val Ser Leu Gln 195 200 205 gac gga gga cag aag gcc gtg aag gac ctg aac ccc gga gac aag gtg 672 Asp Gly Gly Gln Lys Ala Val Lys Asp Leu Asn Pro Gly Asp Lys Val 210 215 220 ctg gcg gca gac agc gcg gga aac ctg gtg ttc agc gac ttc atc atg 720 Leu Ala Ala Asp Ser Ala Gly Asn Leu Val Phe Ser Asp Phe Ile Met 225 230 235 240 ttc aca gac cga gac tcc acg acg cga cgt gtg ttt tac gtc ata gaa 768 Phe Thr Asp Arg Asp Ser Thr Thr Arg Arg Val Phe Tyr Val Ile Glu 245 250 255 acg caa gaa ccc gtt gaa aag atc acc ctc acc gcc gct cac ctc ctt 816 Thr Gln Glu Pro Val Glu Lys Ile Thr Leu Thr Ala Ala His Leu Leu 260 265 270 ttt gtc ctc gac aac tca acg gaa gat ctc cac acc atg acc gcc gcg 864 Phe Val Leu Asp Asn Ser Thr Glu Asp Leu His Thr Met Thr Ala Ala 275 280 285 tat gcc agc agt gtc aga gcc gga caa aag gtg atg gtt gtt gat gat 912 Tyr Ala Ser Ser Val Arg Ala Gly Gln Lys Val Met Val Val Asp Asp 290 295 300 agc ggt cag ctt aaa tct gtc atc gtg cag cgg ata tac acg gag gag 960 Ser Gly Gln Leu Lys Ser Val Ile Val Gln Arg Ile Tyr Thr Glu Glu 305 310 315 320 cag cgg ggc tcg ttc gca cca gtg act gca cat ggg acc att gtg gtc 1008 Gln Arg Gly Ser Phe Ala Pro Val Thr Ala His Gly Thr Ile Val Val 325 330 335 gac aga ata ctg gcg tcc tgt tac gcc gta ata gag gac cag ggg ctt 1056 Asp Arg Ile Leu Ala Ser Cys Tyr Ala Val Ile Glu Asp Gln Gly Leu 340 345 350 gcg cat ttg gcc ttc gcg ccc gcc agg ctc tat tat tac gtg tca tca 1104 Ala His Leu Ala Phe Ala Pro Ala Arg Leu Tyr Tyr Tyr Val Ser Ser 355 360 365 ttc ctg tcc ccc aaa act cca gca gtc ggt cca atg cga ctt tac aac 1152 Phe Leu Ser Pro Lys Thr Pro Ala Val Gly Pro Met Arg Leu Tyr Asn 370 375 380 agg agg ggg tcc act ggt act cca ggc tcc tgt cat caa atg gga acg 1200 Arg Arg Gly Ser Thr Gly Thr Pro Gly Ser Cys His Gln Met Gly Thr 385 390 395 400 tgg ctt ttg gac agc aac atg ctt cat cct ttg ggg atg tca gta aac 1248 Trp Leu Leu Asp Ser Asn Met Leu His Pro Leu Gly Met Ser Val Asn 405 410 415 tca agc tg 1256 Ser Ser 10 1425 DNA Homo sapiens n = a, t, g or c 10 atg ctg ctg ctg gcg aga tgt ctg ctg cta gtc ctc gtc tcc tcg ctg 48 Met Leu Leu Leu Ala Arg Cys Leu Leu Leu Val Leu Val Ser Ser Leu 1 5 10 15 ctg gta tgc tcg gga ctg gcg tgc gga ccg ggc agg ggg ttc ggg aag 96 Leu Val Cys Ser Gly Leu Ala Cys Gly Pro Gly Arg Gly Phe Gly Lys 20 25 30 agg agg cac ccc aaa aag ctg acc cct tta gcc tac aag cag ttt atc 144 Arg Arg His Pro Lys Lys Leu Thr Pro Leu Ala Tyr Lys Gln Phe Ile 35 40 45 ccc aat gtg gcc gag aag acc cta ggc gcc agc gga agg tat gaa ggg 192 Pro Asn Val Ala Glu Lys Thr Leu Gly Ala Ser Gly Arg Tyr Glu Gly 50 55 60 aag atc tcc aga aac tcc gag cga ttt aag gaa ctc acc ccc aat tac 240 Lys Ile Ser Arg Asn Ser Glu Arg Phe Lys Glu Leu Thr Pro Asn Tyr 65 70 75 80 aac ccc gac atc ata ttt aag gat gaa gaa aac acc gga gcg gac agg 288 Asn Pro Asp Ile Ile Phe Lys Asp Glu Glu Asn Thr Gly Ala Asp Arg 85 90 95 ctg atg act cag agg tgt aag gac aag ttg aac gct ttg gcc atc tcg 336 Leu Met Thr Gln Arg Cys Lys Asp Lys Leu Asn Ala Leu Ala Ile Ser 100 105 110 gtg atg aac cag tgg cca gga gtg aaa ctg cgg gtg acc gag ggc tgg 384 Val Met Asn Gln Trp Pro Gly Val Lys Leu Arg Val Thr Glu Gly Trp 115 120 125 gac gaa gat ggc cac cac tca gag gag tct ctg cac tac gag ggc cgc 432 Asp Glu Asp Gly His His Ser Glu Glu Ser Leu His Tyr Glu Gly Arg 130 135 140 gca gtg gac atc acc acg tct gac cgc gac cgc agc aag tac ggc atg 480 Ala Val Asp Ile Thr Thr Ser Asp Arg Asp Arg Ser Lys Tyr Gly Met 145 150 155 160 ctg gcc cgc ctg gcg gtg gag gcc ggc ttc gac tgg gtg tac tac gag 528 Leu Ala Arg Leu Ala Val Glu Ala Gly Phe Asp Trp Val Tyr Tyr Glu 165 170 175 tcc aag gca cat atc cac tgc tcg gtg aaa gca gag aac tcg gtg gcg 576 Ser Lys Ala His Ile His Cys Ser Val Lys Ala Glu Asn Ser Val Ala 180 185 190 gcc aaa tcg gga ggc tgc ttc ccg ggc tcg gcc acg gtg cac ctg gag 624 Ala Lys Ser Gly Gly Cys Phe Pro Gly Ser Ala Thr Val His Leu Glu 195 200 205 cag ggc ggc acc aag ctg gtg aag gac ctg agc ccc ggg gac cgc gtg 672 Gln Gly Gly Thr Lys Leu Val Lys Asp Leu Ser Pro Gly Asp Arg Val 210 215 220 ctg gcg gcg gac gac cag ggc cgg ctg ctc tac agc gac ttc ctc act 720 Leu Ala Ala Asp Asp Gln Gly Arg Leu Leu Tyr Ser Asp Phe Leu Thr 225 230 235 240 ttc ctg gac cgc gac gac ggc gcc aag aag gtc ttc tac gtg atc gag 768 Phe Leu Asp Arg Asp Asp Gly Ala Lys Lys Val Phe Tyr Val Ile Glu 245 250 255 acg cgg gag ccg cgc gag cgc ctg ctg ctc acc gcc gcg cac ctg ctc 816 Thr Arg Glu Pro Arg Glu Arg Leu Leu Leu Thr Ala Ala His Leu Leu 260 265 270 ttt gtg gcg ccg cac aac gac tcg gcc acc ggg gag ccc gag gcg tcc 864 Phe Val Ala Pro His Asn Asp Ser Ala Thr Gly Glu Pro Glu Ala Ser 275 280 285 tcg ggc tcg ggg ccg cct tcc ggg ggc gca ctg ggg cct cgg gcg ctg 912 Ser Gly Ser Gly Pro Pro Ser Gly Gly Ala Leu Gly Pro Arg Ala Leu 290 295 300 ttc gcc agc cgc gtg cgc ccg ggc cag cgc gtg tac gtg gtg gcc gag 960 Phe Ala Ser Arg Val Arg Pro Gly Gln Arg Val Tyr Val Val Ala Glu 305 310 315 320 cgt gac ggg gac cgc cgg ctc ctg ccc gcc gct gtg cac agc gtg acc 1008 Arg Asp Gly Asp Arg Arg Leu Leu Pro Ala Ala Val His Ser Val Thr 325 330 335 cta agc gag gag gcc gcg ggc gcc tac gcg ccg ctc acg gcc cag ggc 1056 Leu Ser Glu Glu Ala Ala Gly Ala Tyr Ala Pro Leu Thr Ala Gln Gly 340 345 350 acc att ctc atc aac cgg gtg ctg gcc tcg tgc tac gcg gtc atc gag 1104 Thr Ile Leu Ile Asn Arg Val Leu Ala Ser Cys Tyr Ala Val Ile Glu 355 360 365 gag cac agc tgg gcg cac cgg gcc ttc gcg ccc ttc cgc ctg gcg cac 1152 Glu His Ser Trp Ala His Arg Ala Phe Ala Pro Phe Arg Leu Ala His 370 375 380 gcg ctc ctg gct gca ctg gcg ccc gcg cgc acg gac cgc ggc ggg gac 1200 Ala Leu Leu Ala Ala Leu Ala Pro Ala Arg Thr Asp Arg Gly Gly Asp 385 390 395 400 agc ggc ggc ggg gac cgc ggg ggc ggc ggc ggc aga gta gcc cta acc 1248 Ser Gly Gly Gly Asp Arg Gly Gly Gly Gly Gly Arg Val Ala Leu Thr 405 410 415 gct cca ggt gct gcc gac gct ccg ggt gcg ggg gcc acc gcg ggc atc 1296 Ala Pro Gly Ala Ala Asp Ala Pro Gly Ala Gly Ala Thr Ala Gly Ile 420 425 430 cac tgg tac tcg cag ctg ctc tac caa ata ggc acc tgg ctc ctg gac 1344 His Trp Tyr Ser Gln Leu Leu Tyr Gln Ile Gly Thr Trp Leu Leu Asp 435 440 445 agc gag gcc ctg cac ccg ctg ggc atg gcg gtc aag tcc agc nnn agc 1392 Ser Glu Ala Leu His Pro Leu Gly Met Ala Val Lys Ser Ser Xaa Ser 450 455 460 cgg ggg gcc ggg gga ggg gcg cgg gag ggg gcc 1425 Arg Gly Ala Gly Gly Gly Ala Arg Glu Gly Ala 465 470 475 11 1622 DNA Homo sapiens CDS (51)..(1283) 11 catcagccca ccaggagacc tcgcccgccg ctcccccggg ctccccggcc atg tct 56 Met Ser 1 ccc gcc cgg ctc cgg ccc cga ctg cac ttc tgc ctg gtc ctg ttg ctg 104 Pro Ala Arg Leu Arg Pro Arg Leu His Phe Cys Leu Val Leu Leu Leu 5 10 15 ctg ctg gtg gtg ccc gcg gca tgg ggc tgc ggg ccg ggt cgg gtg gtg 152 Leu Leu Val Val Pro Ala Ala Trp Gly Cys Gly Pro Gly Arg Val Val 20 25 30 ggc agc cgc cgg cga ccg cca cgc aaa ctc gtg ccg ctc gcc tac aag 200 Gly Ser Arg Arg Arg Pro Pro Arg Lys Leu Val Pro Leu Ala Tyr Lys 35 40 45 50 cag ttc agc ccc aat gtg ccc gag aag acc ctg ggc gcc agc gga cgc 248 Gln Phe Ser Pro Asn Val Pro Glu Lys Thr Leu Gly Ala Ser Gly Arg 55 60 65 tat gaa ggc aag atc gct cgc agc tcc gag cgc ttc aag gag ctc acc 296 Tyr Glu Gly Lys Ile Ala Arg Ser Ser Glu Arg Phe Lys Glu Leu Thr 70 75 80 ccc aat tac aat cca gac atc atc ttc aag gac gag gag aac aca ggc 344 Pro Asn Tyr Asn Pro Asp Ile Ile Phe Lys Asp Glu Glu Asn Thr Gly 85 90 95 gcc gac cgc ctc atg acc cag cgc tgc aag gac cgc ctg aac tcg ctg 392 Ala Asp Arg Leu Met Thr Gln Arg Cys Lys Asp Arg Leu Asn Ser Leu 100 105 110 gct atc tcg gtg atg aac cag tgg ccc ggt gtg aag ctg cgg gtg acc 440 Ala Ile Ser Val Met Asn Gln Trp Pro Gly Val Lys Leu Arg Val Thr 115 120 125 130 gag ggc tgg gac gag gac ggc cac cac tca gag gag tcc ctg cat tat 488 Glu Gly Trp Asp Glu Asp Gly His His Ser Glu Glu Ser Leu His Tyr 135 140 145 gag ggc cgc gcg gtg gac atc acc aca tca gac cgc gac cgc aat aag 536 Glu Gly Arg Ala Val Asp Ile Thr Thr Ser Asp Arg Asp Arg Asn Lys 150 155 160 tat gga ctg ctg gcg cgc ttg gca gtg gag gcc ggc ttt gac tgg gtg 584 Tyr Gly Leu Leu Ala Arg Leu Ala Val Glu Ala Gly Phe Asp Trp Val 165 170 175 tat tac gag tca aag gcc cac gtg cat tgc tcc gtc aag tcc gag cac 632 Tyr Tyr Glu Ser Lys Ala His Val His Cys Ser Val Lys Ser Glu His 180 185 190 tcg gcc gca gcc aag acg ggc ggc tgc ttc cct gcc gga gcc cag gta 680 Ser Ala Ala Ala Lys Thr Gly Gly Cys Phe Pro Ala Gly Ala Gln Val 195 200 205 210 cgc ctg gag agt ggg gcg cgt gtg gcc ttg tca gcc gtg agg ccg gga 728 Arg Leu Glu Ser Gly Ala Arg Val Ala Leu Ser Ala Val Arg Pro Gly 215 220 225 gac cgt gtg ctg gcc atg ggg gag gat ggg agc ccc acc ttc agc gat 776 Asp Arg Val Leu Ala Met Gly Glu Asp Gly Ser Pro Thr Phe Ser Asp 230 235 240 gtg ctc att ttc ctg gac cgc gag ccc cac agg ctg aga gcc ttc cag 824 Val Leu Ile Phe Leu Asp Arg Glu Pro His Arg Leu Arg Ala Phe Gln 245 250 255 gtc atc gag act cag gac ccc cca cgc cgc ctg gca ctc aca ccc gct 872 Val Ile Glu Thr Gln Asp Pro Pro Arg Arg Leu Ala Leu Thr Pro Ala 260 265 270 cac ctg ctc ttt acg gct gac aat cac acg gag ccg gca gcc cgc ttc 920 His Leu Leu Phe Thr Ala Asp Asn His Thr Glu Pro Ala Ala Arg Phe 275 280 285 290 cgg gcc aca ttt gcc agc cac gtg cag cct ggc cag tac gtg ctg gtg 968 Arg Ala Thr Phe Ala Ser His Val Gln Pro Gly Gln Tyr Val Leu Val 295 300 305 gct ggg gtg cca ggc ctg cag cct gcc cgc gtg gca gct gtc tct aca 1016 Ala Gly Val Pro Gly Leu Gln Pro Ala Arg Val Ala Ala Val Ser Thr 310 315 320 cac gtg gcc ctc ggg gcc tac gcc ccg ctc aca aag cat ggg aca ctg 1064 His Val Ala Leu Gly Ala Tyr Ala Pro Leu Thr Lys His Gly Thr Leu 325 330 335 gtg gtg gag gat gtg gtg gca tcc tgc ttc gcg gcc gtg gct gac cac 1112 Val Val Glu Asp Val Val Ala Ser Cys Phe Ala Ala Val Ala Asp His 340 345 350 cac ctg gct cag ttg gcc ttc tgg ccc ctg aga ctc ttt cac agc ttg 1160 His Leu Ala Gln Leu Ala Phe Trp Pro Leu Arg Leu Phe His Ser Leu 355 360 365 370 gca tgg ggc agc tgg acc ccg ggg gag ggt gtg cat tgg tac ccc cag 1208 Ala Trp Gly Ser Trp Thr Pro Gly Glu Gly Val His Trp Tyr Pro Gln 375 380 385 ctg ctc tac cgc ctg ggg cgt ctc ctg cta gaa gag ggc agc ttc cac 1256 Leu Leu Tyr Arg Leu Gly Arg Leu Leu Leu Glu Glu Gly Ser Phe His 390 395 400 cca ctg ggc atg tcc ggg gca ggg agc tgaaaggact ccaccgctgc 1303 Pro Leu Gly Met Ser Gly Ala Gly Ser 405 410 cctcctggaa ctgctgtact gggtccagaa gcctctcagc caggagggag ctggccctgg 1363 aagggacctg agctggggga cactggctcc tgccatctcc tctgccatga agatacacca 1423 ttgagacttg actgggcaac accagcgtcc cccacccgcg tcgtggtgta gtcatagagc 1483 tgcaagctga gctggcgagg ggatggttgt tgacccctct ctcctagaga ccttgaggct 1543 ggcacggcga ctcccaactc agcctgctct cactacgagt tttcatactc tgcctccccc 1603 attgggaggg cccattccc 1622 12 1190 DNA Homo sapiens CDS (1)..(1188) 12 atg gct ctc ctg acc aat cta ctg ccc ttg tgc tgc ttg gca ctt ctg 48 Met Ala Leu Leu Thr Asn Leu Leu Pro Leu Cys Cys Leu Ala Leu Leu 1 5 10 15 gcg ctg cca gcc cag agc tgc ggg ccg ggc cgg ggg ccg gtt ggc cgg 96 Ala Leu Pro Ala Gln Ser Cys Gly Pro Gly Arg Gly Pro Val Gly Arg 20 25 30 cgc cgc tat gcg cgc aag cag ctc gtg ccg cta ctc tac aag caa ttt 144 Arg Arg Tyr Ala Arg Lys Gln Leu Val Pro Leu Leu Tyr Lys Gln Phe 35 40 45 gtg ccc ggc gtg cca gag cgg acc ctg ggc gcc agt ggg cca gcg gag 192 Val Pro Gly Val Pro Glu Arg Thr Leu Gly Ala Ser Gly Pro Ala Glu 50 55 60 ggg agg gtg gca agg ggc tcc gag cgc ttc cgg gac ctc gtg ccc aac 240 Gly Arg Val Ala Arg Gly Ser Glu Arg Phe Arg Asp Leu Val Pro Asn 65 70 75 80 tac aac ccc gac atc atc ttc aag gat gag gag aac agt gga gcc gac 288 Tyr Asn Pro Asp Ile Ile Phe Lys Asp Glu Glu Asn Ser Gly Ala Asp 85 90 95 cgc ctg atg acc gag cgt tgc aag gag agg gtg aac gct ttg gcc att 336 Arg Leu Met Thr Glu Arg Cys Lys Glu Arg Val Asn Ala Leu Ala Ile 100 105 110 gcc gtg atg aac atg tgg ccc gga gtg cgc cta cga gtg act gag ggc 384 Ala Val Met Asn Met Trp Pro Gly Val Arg Leu Arg Val Thr Glu Gly 115 120 125 tgg gac gag gac ggc cac cac gct cag gat tca ctc cac tac gaa ggc 432 Trp Asp Glu Asp Gly His His Ala Gln Asp Ser Leu His Tyr Glu Gly 130 135 140 cgt gct ttg gac atc act acg tct gac cgc gac cgc aac aag tat ggg 480 Arg Ala Leu Asp Ile Thr Thr Ser Asp Arg Asp Arg Asn Lys Tyr Gly 145 150 155 160 ttg ctg gcg cgc ctc gca gtg gaa gcc ggc ttc gac tgg gtc tac tac 528 Leu Leu Ala Arg Leu Ala Val Glu Ala Gly Phe Asp Trp Val Tyr Tyr 165 170 175 gag tcc cgc aac cac gtc cac gtg tcg gtc aaa gct gat aac tca ctg 576 Glu Ser Arg Asn His Val His Val Ser Val Lys Ala Asp Asn Ser Leu 180 185 190 gcg gtc cgg gcg ggc ggc tgc ttt ccg gga aat gca act gtg cgc ctg 624 Ala Val Arg Ala Gly Gly Cys Phe Pro Gly Asn Ala Thr Val Arg Leu 195 200 205 tgg agc ggc gag cgg aaa ggg ctg cgg gaa ctg cac cgc gga gac tgg 672 Trp Ser Gly Glu Arg Lys Gly Leu Arg Glu Leu His Arg Gly Asp Trp 210 215 220 gtt ttg gcg gcc gat gcg tca ggc cgg gtg gtg ccc acg ccg gtg ctg 720 Val Leu Ala Ala Asp Ala Ser Gly Arg Val Val Pro Thr Pro Val Leu 225 230 235 240 ctc ttc ctg gac cgg gac ttg cag cgc cgg gct tca ttt gtg gct gtg 768 Leu Phe Leu Asp Arg Asp Leu Gln Arg Arg Ala Ser Phe Val Ala Val 245 250 255 gag acc gag tgg cct cca cgc aaa ctg ttg ctc acg ccc tgg cac ctg 816 Glu Thr Glu Trp Pro Pro Arg Lys Leu Leu Leu Thr Pro Trp His Leu 260 265 270 gtg ttt gcc gct cga ggg ccg gcg ccc gcg cca ggc gac ttt gca ccg 864 Val Phe Ala Ala Arg Gly Pro Ala Pro Ala Pro Gly Asp Phe Ala Pro 275 280 285 gtg ttc gcg cgc cgg cta cgc gct ggg gac tcg gtg ctg gcg ccc ggc 912 Val Phe Ala Arg Arg Leu Arg Ala Gly Asp Ser Val Leu Ala Pro Gly 290 295 300 ggg gat gcg ctt cgg cca gcg cgc gtg gcc cgt gtg gcg cgg gag gaa 960 Gly Asp Ala Leu Arg Pro Ala Arg Val Ala Arg Val Ala Arg Glu Glu 305 310 315 320 gcc gtg ggc gtg ttc gcg ccg ctc acc gcg cac ggg acg ctg ctg gtg 1008 Ala Val Gly Val Phe Ala Pro Leu Thr Ala His Gly Thr Leu Leu Val 325 330 335 aac gat gtc ctg gcc tct tgc tac gcg gtt ctg gag agt cac cag tgg 1056 Asn Asp Val Leu Ala Ser Cys Tyr Ala Val Leu Glu Ser His Gln Trp 340 345 350 gcg cac cgc gct ttt gcc ccc ttg aga ctg ctg cac gcg cta ggg gcg 1104 Ala His Arg Ala Phe Ala Pro Leu Arg Leu Leu His Ala Leu Gly Ala 355 360 365 ctg ctc ccc ggc ggg gcc gtc cag ccg act ggc atg cat tgg tac tct 1152 Leu Leu Pro Gly Gly Ala Val Gln Pro Thr Gly Met His Trp Tyr Ser 370 375 380 cgg ctc ctc tac cgc tta gcg gag gag cta ctg ggc tg 1190 Arg Leu Leu Tyr Arg Leu Ala Glu Glu Leu Leu Gly 385 390 395 13 1251 DNA Brachydanio rerio CDS (1)..(1248) 13 atg gac gta agg ctg cat ctg aag caa ttt gct tta ctg tgt ttt atc 48 Met Asp Val Arg Leu His Leu Lys Gln Phe Ala Leu Leu Cys Phe Ile 1 5 10 15 agc ttg ctt ctg acg cct tgt gga tta gcc tgt ggt cct ggt aga ggt 96 Ser Leu Leu Leu Thr Pro Cys Gly Leu Ala Cys Gly Pro Gly Arg Gly 20 25 30 tat gga aaa cga aga cac cca aag aaa tta acc ccg ttg gct tac aag 144 Tyr Gly Lys Arg Arg His Pro Lys Lys Leu Thr Pro Leu Ala Tyr Lys 35 40 45 caa ttc atc ccc aac gtt gct gag aaa acg ctt gga gcc agc ggc aaa 192 Gln Phe Ile Pro Asn Val Ala Glu Lys Thr Leu Gly Ala Ser Gly Lys 50 55 60 tac gaa ggc aaa atc aca agg aat tca gag aga ttt aaa gag ctg att 240 Tyr Glu Gly Lys Ile Thr Arg Asn Ser Glu Arg Phe Lys Glu Leu Ile 65 70 75 80 ccg aat tat aat ccc gat atc atc ttt aag gac gag gaa aac aca aac 288 Pro Asn Tyr Asn Pro Asp Ile Ile Phe Lys Asp Glu Glu Asn Thr Asn 85 90 95 gct gac agg ctg atg acc aag cgc tgt aag gac aag tta aat tcg ttg 336 Ala Asp Arg Leu Met Thr Lys Arg Cys Lys Asp Lys Leu Asn Ser Leu 100 105 110 gcc ata tcc gtc atg aac cac tgg ccc ggc gtg aaa ctg cgc gtc act 384 Ala Ile Ser Val Met Asn His Trp Pro Gly Val Lys Leu Arg Val Thr 115 120 125 gaa ggc tgg gat gag gat ggt cac cat tta gaa gaa tct ttg cac tat 432 Glu Gly Trp Asp Glu Asp Gly His His Leu Glu Glu Ser Leu His Tyr 130 135 140 gag gga cgg gca gtg gac atc act acc tca gac agg gat aaa agc aag 480 Glu Gly Arg Ala Val Asp Ile Thr Thr Ser Asp Arg Asp Lys Ser Lys 145 150 155 160 tat ggg atg cta tcc agg ctt gca gtg gag gca gga ttc gac tgg gtc 528 Tyr Gly Met Leu Ser Arg Leu Ala Val Glu Ala Gly Phe Asp Trp Val 165 170 175 tat tat gaa tct aaa gcc cac ata cac tgc tct gtc aaa gca gaa aat 576 Tyr Tyr Glu Ser Lys Ala His Ile His Cys Ser Val Lys Ala Glu Asn 180 185 190 tca gtg gct gct aaa tca gga gga tgt ttt cct ggg tct ggg acg gtg 624 Ser Val Ala Ala Lys Ser Gly Gly Cys Phe Pro Gly Ser Gly Thr Val 195 200 205 aca ctt ggt gat ggg acg agg aaa ccc atc aaa gat ctt aaa gtg ggc 672 Thr Leu Gly Asp Gly Thr Arg Lys Pro Ile Lys Asp Leu Lys Val Gly 210 215 220 gac cgg gtt ttg gct gca gac gag aag gga aat gtc tta ata agc gac 720 Asp Arg Val Leu Ala Ala Asp Glu Lys Gly Asn Val Leu Ile Ser Asp 225 230 235 240 ttt att atg ttt ata gac cac gat ccg aca acg aga agg caa ttc atc 768 Phe Ile Met Phe Ile Asp His Asp Pro Thr Thr Arg Arg Gln Phe Ile 245 250 255 gtc atc gag acg tca gaa cct ttc acc aag ctc acc ctc act gcc gcg 816 Val Ile Glu Thr Ser Glu Pro Phe Thr Lys Leu Thr Leu Thr Ala Ala 260 265 270 cac cta gtt ttc gtt gga aac tct tca gca gct tcg ggt ata aca gca 864 His Leu Val Phe Val Gly Asn Ser Ser Ala Ala Ser Gly Ile Thr Ala 275 280 285 aca ttt gcc agc aac gtg aag cct gga gat aca gtt tta gtg tgg gaa 912 Thr Phe Ala Ser Asn Val Lys Pro Gly Asp Thr Val Leu Val Trp Glu 290 295 300 gac aca tgc gag agc ctc aag agc gtt aca gtg aaa agg att tac act 960 Asp Thr Cys Glu Ser Leu Lys Ser Val Thr Val Lys Arg Ile Tyr Thr 305 310 315 320 gag gag cac gag ggc tct ttt gcg cca gtc acc gcg cac gga acc ata 1008 Glu Glu His Glu Gly Ser Phe Ala Pro Val Thr Ala His Gly Thr Ile 325 330 335 ata gtg gat cag gtg ttg gca tcg tgc tac gcg gtc att gag aac cac 1056 Ile Val Asp Gln Val Leu Ala Ser Cys Tyr Ala Val Ile Glu Asn His 340 345 350 aaa tgg gca cat tgg gct ttt gcg ccg gtc agg ttg tgt cac aag ctg 1104 Lys Trp Ala His Trp Ala Phe Ala Pro Val Arg Leu Cys His Lys Leu 355 360 365 atg acg tgg ctt ttt ccg gct cgt gaa tca aac gtc aat ttt cag gag 1152 Met Thr Trp Leu Phe Pro Ala Arg Glu Ser Asn Val Asn Phe Gln Glu 370 375 380 gat ggt atc cac tgg tac tca aat atg ctg ttt cac atc ggc tct tgg 1200 Asp Gly Ile His Trp Tyr Ser Asn Met Leu Phe His Ile Gly Ser Trp 385 390 395 400 ctg ctg gac aga gac tct ttc cat cca ctc ggg att tta cac tta agt 1248 Leu Leu Asp Arg Asp Ser Phe His Pro Leu Gly Ile Leu His Leu Ser 405 410 415 tga 1251 14 1416 DNA Drosophilia sp. CDS (1)..(1413) 14 atg gat aac cac agc tca gtg cct tgg gcc agt gcc gcc agt gtc acc 48 Met Asp Asn His Ser Ser Val Pro Trp Ala Ser Ala Ala Ser Val Thr 1 5 10 15 tgt ctc tcc ctg gga tgc caa atg cca cag ttc cag ttc cag ttc cag 96 Cys Leu Ser Leu Gly Cys Gln Met Pro Gln Phe Gln Phe Gln Phe Gln 20 25 30 ctc caa atc cgc agc gag ctc cat ctc cgc aag ccc gca aga aga acg 144 Leu Gln Ile Arg Ser Glu Leu His Leu Arg Lys Pro Ala Arg Arg Thr 35 40 45 caa acg atg cgc cac att gcg cat acg cag cgt tgc ctc agc agg ctg 192 Gln Thr Met Arg His Ile Ala His Thr Gln Arg Cys Leu Ser Arg Leu 50 55 60 acc tct ctg gtg gcc ctg ctg ctg atc gtc ttg ccg atg gtc ttt agc 240 Thr Ser Leu Val Ala Leu Leu Leu Ile Val Leu Pro Met Val Phe Ser 65 70 75 80 ccg gct cac agc tgc ggt cct ggc cga gga ttg ggt cgt cat agg gcg 288 Pro Ala His Ser Cys Gly Pro Gly Arg Gly Leu Gly Arg His Arg Ala 85 90 95 cgc aac ctg tat ccg ctg gtc ctc aag cag aca att ccc aat cta tcc 336 Arg Asn Leu Tyr Pro Leu Val Leu Lys Gln Thr Ile Pro Asn Leu Ser 100 105 110 gag tac acg aac agc gcc tcc gga cct ctg gag ggt gtg atc cgt cgg 384 Glu Tyr Thr Asn Ser Ala Ser Gly Pro Leu Glu Gly Val Ile Arg Arg 115 120 125 gat tcg ccc aaa ttc aag gac ctc gtg ccc aac tac aac agg gac atc 432 Asp Ser Pro Lys Phe Lys Asp Leu Val Pro Asn Tyr Asn Arg Asp Ile 130 135 140 ctt ttc cgt gac gag gaa ggc acc gga gcg gat ggc ttg atg agc aag 480 Leu Phe Arg Asp Glu Glu Gly Thr Gly Ala Asp Gly Leu Met Ser Lys 145 150 155 160 cgc tgc aag gag aag cta aac gtg ctg gcc tac tcg gtg atg aac gaa 528 Arg Cys Lys Glu Lys Leu Asn Val Leu Ala Tyr Ser Val Met Asn Glu 165 170 175 tgg ccc ggc atc cgg ctg ctg gtc acc gag agc tgg gac gag gac tac 576 Trp Pro Gly Ile Arg Leu Leu Val Thr Glu Ser Trp Asp Glu Asp Tyr 180 185 190 cat cac ggc cag gag tcg ctc cac tac gag ggc cga gcg gtg acc att 624 His His Gly Gln Glu Ser Leu His Tyr Glu Gly Arg Ala Val Thr Ile 195 200 205 gcc acc tcc gat cgc gac cag tcc aaa tac ggc atg ctc gct cgc ctg 672 Ala Thr Ser Asp Arg Asp Gln Ser Lys Tyr Gly Met Leu Ala Arg Leu 210 215 220 gcc gtc gag gct gga ttc gat tgg gtc tcc tac gtc agc agg cgc cac 720 Ala Val Glu Ala Gly Phe Asp Trp Val Ser Tyr Val Ser Arg Arg His 225 230 235 240 atc tac tgc tcc gtc aag tca gat tcg tcg atc agt tcc cac gtg cac 768 Ile Tyr Cys Ser Val Lys Ser Asp Ser Ser Ile Ser Ser His Val His 245 250 255 ggc tgc ttc acg ccg gag agc aca gcg ctg ctg gag agt gga gtc cgg 816 Gly Cys Phe Thr Pro Glu Ser Thr Ala Leu Leu Glu Ser Gly Val Arg 260 265 270 aag ccg ctc ggc gag ctc tct atc gga gat cgt gtt ttg agc atg acc 864 Lys Pro Leu Gly Glu Leu Ser Ile Gly Asp Arg Val Leu Ser Met Thr 275 280 285 gcc aac gga cag gcc gtc tac agc gaa gtg atc ctc ttc atg gac cgc 912 Ala Asn Gly Gln Ala Val Tyr Ser Glu Val Ile Leu Phe Met Asp Arg 290 295 300 aac ctc gag cag atg caa aac ttt gtg cag ctg cac acg gac ggt gga 960 Asn Leu Glu Gln Met Gln Asn Phe Val Gln Leu His Thr Asp Gly Gly 305 310 315 320 gca gtg ctc acg gtg acg ccg gct cac ctg gtt agc gtt tgg cag ccg 1008 Ala Val Leu Thr Val Thr Pro Ala His Leu Val Ser Val Trp Gln Pro 325 330 335 gag agc cag aag ctc acg ttt gtg ttt gcg cat cgc atc gag gag aag 1056 Glu Ser Gln Lys Leu Thr Phe Val Phe Ala His Arg Ile Glu Glu Lys 340 345 350 aac cag gtg ctc gta cgg gat gtg gag acg ggc gag ctg agg ccc cag 1104 Asn Gln Val Leu Val Arg Asp Val Glu Thr Gly Glu Leu Arg Pro Gln 355 360 365 cga gtg gtc aag ttg ggc agt gtg cgc agt aag ggc gtg gtc gcg ccg 1152 Arg Val Val Lys Leu Gly Ser Val Arg Ser Lys Gly Val Val Ala Pro 370 375 380 ctg acc cgc gag ggc acc att gtg gtc aac tcg gtg gcc gcc agt tgc 1200 Leu Thr Arg Glu Gly Thr Ile Val Val Asn Ser Val Ala Ala Ser Cys 385 390 395 400 tat gcg gtg atc aac agt cag tcg ctg gcc cac tgg gga ctg gct ccc 1248 Tyr Ala Val Ile Asn Ser Gln Ser Leu Ala His Trp Gly Leu Ala Pro 405 410 415 atg cgc ctg ctg tcc acg ctg gag gcg tgg ctg ccc gcc aag gag cag 1296 Met Arg Leu Leu Ser Thr Leu Glu Ala Trp Leu Pro Ala Lys Glu Gln 420 425 430 ttg cac agt tcg ccg aag gtg gtg agc tcg gcg cag cag cag aat ggc 1344 Leu His Ser Ser Pro Lys Val Val Ser Ser Ala Gln Gln Gln Asn Gly 435 440 445 atc cat tgg tat gcc aat gcg ctc tac aag gtc aag gac tac gtg ctg 1392 Ile His Trp Tyr Ala Asn Ala Leu Tyr Lys Val Lys Asp Tyr Val Leu 450 455 460 ccg cag agc tgg cgc cac gat tga 1416 Pro Gln Ser Trp Arg His Asp 465 470 15 221 PRT Artificial Sequence Description of Artificial Sequence Consensus sequence 15 Cys Gly Pro Gly Arg Gly Xaa Gly Xaa Arg Arg His Pro Lys Lys Leu 1 5 10 15 Thr Pro Leu Ala Tyr Lys Gln Phe Ile Pro Asn Val Ala Glu Lys Thr 20 25 30 Leu Gly Ala Ser Gly Arg Tyr Glu Gly Lys Ile Xaa Arg Asn Ser Glu 35 40 45 Arg Phe Lys Glu Leu Thr Pro Asn Tyr Asn Pro Asp Ile Ile Phe Lys 50 55 60 Asp Glu Glu Asn Thr Gly Ala Asp Arg Leu Met Thr Gln Arg Cys Lys 65 70 75 80 Asp Lys Leu Asn Xaa Leu Ala Ile Ser Val Met Asn Xaa Trp Pro Gly 85 90 95 Val Xaa Leu Arg Val Thr Glu Gly Trp Asp Glu Asp Gly His His Xaa 100 105 110 Glu Glu Ser Leu His Tyr Glu Gly Arg Ala Val Asp Ile Thr Thr Ser 115 120 125 Asp Arg Asp Xaa Ser Lys Tyr Gly Xaa Leu Xaa Arg Leu Ala Val Glu 130 135 140 Ala Gly Phe Asp Trp Val Tyr Tyr Glu Ser Lys Ala His Ile His Cys 145 150 155 160 Ser Val Lys Ala Glu Asn Ser Val Ala Ala Lys Ser Gly Gly Cys Phe 165 170 175 Pro Gly Ser Ala Xaa Val Xaa Leu Xaa Xaa Gly Gly Xaa Lys Xaa Val 180 185 190 Lys Asp Leu Xaa Pro Gly Asp Xaa Val Leu Ala Ala Asp Xaa Xaa Gly 195 200 205 Xaa Leu Xaa Xaa Ser Asp Phe Xaa Xaa Phe Xaa Asp Arg 210 215 220 16 167 PRT Artificial Sequence Description of Artificial Sequence Consensus sequence 16 Cys Gly Pro Gly Arg Gly Xaa Xaa Xaa Arg Arg Xaa Xaa Xaa Pro Lys 1 5 10 15 Xaa Leu Xaa Pro Leu Xaa Tyr Lys Gln Phe Xaa Pro Xaa Xaa Xaa Glu 20 25 30 Xaa Thr Leu Gly Ala Ser Gly Xaa Xaa Glu Gly Xaa Xaa Xaa Arg Xaa 35 40 45 Ser Glu Arg Phe Xaa Xaa Leu Thr Pro Asn Tyr Asn Pro Asp Ile Ile 50 55 60 Phe Lys Asp Glu Glu Asn Xaa Gly Ala Asp Arg Leu Met Thr Xaa Arg 65 70 75 80 Cys Lys Xaa Xaa Xaa Asn Xaa Leu Ala Ile Ser Val Met Asn Xaa Trp 85 90 95 Pro Gly Val Xaa Leu Arg Val Thr Glu Gly Xaa Asp Glu Asp Gly His 100 105 110 His Xaa Xaa Xaa Ser Leu His Tyr Glu Gly Arg Ala Xaa Asp Ile Thr 115 120 125 Thr Ser Asp Arg Asp Xaa Xaa Lys Tyr Gly Xaa Leu Xaa Arg Leu Ala 130 135 140 Val Glu Ala Gly Phe Asp Trp Val Tyr Tyr Glu Ser Xaa Xaa His Xaa 145 150 155 160 His Xaa Ser Val Lys Xaa Xaa 165 17 425 PRT Gallus sp. 17 Met Val Glu Met Leu Leu Leu Thr Arg Ile Leu Leu Val Gly Phe Ile 1 5 10 15 Cys Ala Leu Leu Val Ser Ser Gly Leu Thr Cys Gly Pro Gly Arg Gly 20 25 30 Ile Gly Lys Arg Arg His Pro Lys Lys Leu Thr Pro Leu Ala Tyr Lys 35 40 45 Gln Phe Ile Pro Asn Val Ala Glu Lys Thr Leu Gly Ala Ser Gly Arg 50 55 60 Tyr Glu Gly Lys Ile Thr Arg Asn Ser Glu Arg Phe Lys Glu Leu Thr 65 70 75 80 Pro Asn Tyr Asn Pro Asp Ile Ile Phe Lys Asp Glu Glu Asn Thr Gly 85 90 95 Ala Asp Arg Leu Met Thr Gln Arg Cys Lys Asp Lys Leu Asn Ala Leu 100 105 110 Ala Ile Ser Val Met Asn Gln Trp Pro Gly Val Lys Leu Arg Val Thr 115 120 125 Glu Gly Trp Asp Glu Asp Gly His His Ser Glu Glu Ser Leu His Tyr 130 135 140 Glu Gly Arg Ala Val Asp Ile Thr Thr Ser Asp Arg Asp Arg Ser Lys 145 150 155 160 Tyr Gly Met Leu Ala Arg Leu Ala Val Glu Ala Gly Phe Asp Trp Val 165 170 175 Tyr Tyr Glu Ser Lys Ala His Ile His Cys Ser Val Lys Ala Glu Asn 180 185 190 Ser Val Ala Ala Lys Ser Gly Gly Cys Phe Pro Gly Ser Ala Thr Val 195 200 205 His Leu Glu His Gly Gly Thr Lys Leu Val Lys Asp Leu Ser Pro Gly 210 215 220 Asp Arg Val Leu Ala Ala Asp Ala Asp Gly Arg Leu Leu Tyr Ser Asp 225 230 235 240 Phe Leu Thr Phe Leu Asp Arg Met Asp Ser Ser Arg Lys Leu Phe Tyr 245 250 255 Val Ile Glu Thr Arg Gln Pro Arg Ala Arg Leu Leu Leu Thr Ala Ala 260 265 270 His Leu Leu Phe Val Ala Pro Gln His Asn Gln Ser Glu Ala Thr Gly 275 280 285 Ser Thr Ser Gly Gln Ala Leu Phe Ala Ser Asn Val Lys Pro Gly Gln 290 295 300 Arg Val Tyr Val Leu Gly Glu Gly Gly Gln Gln Leu Leu Pro Ala Ser 305 310 315 320 Val His Ser Val Ser Leu Arg Glu Glu Ala Ser Gly Ala Tyr Ala Pro 325 330 335 Leu Thr Ala Gln Gly Thr Ile Leu Ile Asn Arg Val Leu Ala Ser Cys 340 345 350 Tyr Ala Val Ile Glu Glu His Ser Trp Ala His Trp Ala Phe Ala Pro 355 360 365 Phe Arg Leu Ala Gln Gly Leu Leu Ala Ala Leu Cys Pro Asp Gly Ala 370 375 380 Ile Pro Thr Ala Ala Thr Thr Thr Thr Gly Ile His Trp Tyr Ser Arg 385 390 395 400 Leu Leu Tyr Arg Ile Gly Ser Trp Val Leu Asp Gly Asp Ala Leu His 405 410 415 Pro Leu Gly Met Val Ala Pro Ala Ser 420 425 18 396 PRT Murine sp. 18 Met Ala Leu Pro Ala Ser Leu Leu Pro Leu Cys Cys Leu Ala Leu Leu 1 5 10 15 Ala Leu Ser Ala Gln Ser Cys Gly Pro Gly Arg Gly Pro Val Gly Arg 20 25 30 Arg Arg Tyr Val Arg Lys Gln Leu Val Pro Leu Leu Tyr Lys Gln Phe 35 40 45 Val Pro Ser Met Pro Glu Arg Thr Leu Gly Ala Ser Gly Pro Ala Glu 50 55 60 Gly Arg Val Thr Arg Gly Ser Glu Arg Phe Arg Asp Leu Val Pro Asn 65 70 75 80 Tyr Asn Pro Asp Ile Ile Phe Lys Asp Glu Glu Asn Ser Gly Ala Asp 85 90 95 Arg Leu Met Thr Glu Arg Cys Lys Glu Arg Val Asn Ala Leu Ala Ile 100 105 110 Ala Val Met Asn Met Trp Pro Gly Val Arg Leu Arg Val Thr Glu Gly 115 120 125 Trp Asp Glu Asp Gly His His Ala Gln Asp Ser Leu His Tyr Glu Gly 130 135 140 Arg Ala Leu Asp Ile Thr Thr Ser Asp Arg Asp Arg Asn Lys Tyr Gly 145 150 155 160 Leu Leu Ala Arg Leu Ala Val Glu Ala Gly Phe Asp Trp Val Tyr Tyr 165 170 175 Glu Ser Arg Asn His Ile His Val Ser Val Lys Ala Asp Asn Ser Leu 180 185 190 Ala Val Arg Ala Gly Gly Cys Phe Pro Gly Asn Ala Thr Val Arg Leu 195 200 205 Arg Ser Gly Glu Arg Lys Gly Leu Arg Glu Leu His Arg Gly Asp Trp 210 215 220 Val Leu Ala Ala Asp Ala Ala Gly Arg Val Val Pro Thr Pro Val Leu 225 230 235 240 Leu Phe Leu Asp Arg Asp Leu Gln Arg Arg Ala Ser Phe Val Ala Val 245 250 255 Glu Thr Glu Arg Pro Pro Arg Lys Leu Leu Leu Thr Pro Trp His Leu 260 265 270 Val Phe Ala Ala Arg Gly Pro Ala Pro Ala Pro Gly Asp Phe Ala Pro 275 280 285 Val Phe Ala Arg Arg Leu Arg Ala Gly Asp Ser Val Leu Ala Pro Gly 290 295 300 Gly Asp Ala Leu Gln Pro Ala Arg Val Ala Arg Val Ala Arg Glu Glu 305 310 315 320 Ala Val Gly Val Phe Ala Pro Leu Thr Ala His Gly Thr Leu Leu Val 325 330 335 Asn Asp Val Leu Ala Ser Cys Tyr Ala Val Leu Glu Ser His Gln Trp 340 345 350 Ala His Arg Ala Phe Ala Pro Leu Arg Leu Leu His Ala Leu Gly Ala 355 360 365 Leu Leu Pro Gly Gly Ala Val Gln Pro Thr Gly Met His Trp Tyr Ser 370 375 380 Arg Leu Leu Tyr Arg Leu Ala Glu Glu Leu Met Gly 385 390 395 19 411 PRT Murine sp. 19 Met Ser Pro Ala Trp Leu Arg Pro Arg Leu Arg Phe Cys Leu Phe Leu 1 5 10 15 Leu Leu Leu Leu Leu Val Pro Ala Ala Arg Gly Cys Gly Pro Gly Arg 20 25 30 Val Val Gly Ser Arg Arg Arg Pro Pro Arg Lys Leu Val Pro Leu Ala 35 40 45 Tyr Lys Gln Phe Ser Pro Asn Val Pro Glu Lys Thr Leu Gly Ala Ser 50 55 60 Gly Arg Tyr Glu Gly Lys Ile Ala Arg Ser Ser Glu Arg Phe Lys Glu 65 70 75 80 Leu Thr Pro Asn Tyr Asn Pro Asp Ile Ile Phe Lys Asp Glu Glu Asn 85 90 95 Thr Gly Ala Asp Arg Leu Met Thr Gln Arg Cys Lys Asp Arg Leu Asn 100 105 110 Ser Leu Ala Ile Ser Val Met Asn Gln Trp Pro Gly Val Lys Leu Arg 115 120 125 Val Thr Glu Gly Arg Asp Glu Asp Gly His His Ser Glu Glu Ser Leu 130 135 140 His Tyr Glu Gly Arg Ala Val Asp Ile Thr Thr Ser Asp Arg Asp Arg 145 150 155 160 Asn Lys Tyr Gly Leu Leu Ala Arg Leu Ala Val Glu Ala Gly Phe Asp 165 170 175 Trp Val Tyr Tyr Glu Ser Lys Ala His Val His Cys Ser Val Lys Ser 180 185 190 Glu His Ser Ala Ala Ala Lys Thr Gly Gly Cys Phe Pro Ala Gly Ala 195 200 205 Gln Val Arg Leu Glu Asn Gly Glu Arg Val Ala Leu Ser Ala Val Lys 210 215 220 Pro Gly Asp Arg Val Leu Ala Met Gly Glu Asp Gly Thr Pro Thr Phe 225 230 235 240 Ser Asp Val Leu Ile Phe Leu Asp Arg Glu Pro Asn Arg Leu Arg Ala 245 250 255 Phe Gln Val Ile Glu Thr Gln Asp Pro Pro Arg Arg Leu Ala Leu Thr 260 265 270 Pro Ala His Leu Leu Phe Ile Ala Asp Asn His Thr Glu Pro Ala Ala 275 280 285 His Phe Arg Ala Thr Phe Ala Ser His Val Gln Pro Gly Gln Tyr Val 290 295 300 Leu Val Ser Gly Val Pro Gly Leu Gln Pro Ala Arg Val Ala Ala Val 305 310 315 320 Ser Thr His Val Ala Leu Gly Ser Tyr Ala Pro Leu Thr Arg His Gly 325 330 335 Thr Leu Val Val Glu Asp Val Val Ala Ser Cys Phe Ala Ala Val Ala 340 345 350 Asp His His Leu Ala Gln Leu Ala Phe Trp Pro Leu Arg Leu Phe Pro 355 360 365 Ser Leu Ala Trp Gly Ser Trp Thr Pro Ser Glu Gly Val His Ser Tyr 370 375 380 Pro Gln Met Leu Tyr Arg Leu Gly Arg Leu Leu Leu Glu Glu Ser Thr 385 390 395 400 Phe His Pro Leu Gly Met Ser Gly Ala Gly Ser 405 410 20 437 PRT Murine sp. 20 Met Leu Leu Leu Leu Ala Arg Cys Phe Leu Val Ile Leu Ala Ser Ser 1 5 10 15 Leu Leu Val Cys Pro Gly Leu Ala Cys Gly Pro Gly Arg Gly Phe Gly 20 25 30 Lys Arg Arg His Pro Lys Lys Leu Thr Pro Leu Ala Tyr Lys Gln Phe 35 40 45 Ile Pro Asn Val Ala Glu Lys Thr Leu Gly Ala Ser Gly Arg Tyr Glu 50 55 60 Gly Lys Ile Thr Arg Asn Ser Glu Arg Phe Lys Glu Leu Thr Pro Asn 65 70 75 80 Tyr Asn Pro Asp Ile Ile Phe Lys Asp Glu Glu Asn Thr Gly Ala Asp 85 90 95 Arg Leu Met Thr Gln Arg Cys Lys Asp Lys Leu Asn Ala Leu Ala Ile 100 105 110 Ser Val Met Asn Gln Trp Pro Gly Val Arg Leu Arg Val Thr Glu Gly 115 120 125 Trp Asp Glu Asp Gly His His Ser Glu Glu Ser Leu His Tyr Glu Gly 130 135 140 Arg Ala Val Asp Ile Thr Thr Ser Asp Arg Asp Arg Ser Lys Tyr Gly 145 150 155 160 Met Leu Ala Arg Leu Ala Val Glu Ala Gly Phe Asp Trp Val Tyr Tyr 165 170 175 Glu Ser Lys Ala His Ile His Cys Ser Val Lys Ala Glu Asn Ser Val 180 185 190 Ala Ala Lys Ser Gly Gly Cys Phe Pro Gly Ser Ala Thr Val His Leu 195 200 205 Glu Gln Gly Gly Thr Lys Leu Val Lys Asp Leu Arg Pro Gly Asp Arg 210 215 220 Val Leu Ala Ala Asp Asp Gln Gly Arg Leu Leu Tyr Ser Asp Phe Leu 225 230 235 240 Thr Phe Leu Asp Arg Asp Glu Gly Ala Lys Lys Val Phe Tyr Val Ile 245 250 255 Glu Thr Leu Glu Pro Arg Glu Arg Leu Leu Leu Thr Ala Ala His Leu 260 265 270 Leu Phe Val Ala Pro His Asn Asp Ser Gly Pro Thr Pro Gly Pro Ser 275 280 285 Ala Leu Phe Ala Ser Arg Val Arg Pro Gly Gln Arg Val Tyr Val Val 290 295 300 Ala Glu Arg Gly Gly Asp Arg Arg Leu Leu Pro Ala Ala Val His Ser 305 310 315 320 Val Thr Leu Arg Glu Glu Glu Ala Gly Ala Tyr Ala Pro Leu Thr Ala 325 330 335 His Gly Thr Ile Leu Ile Asn Arg Val Leu Ala Ser Cys Tyr Ala Val 340 345 350 Ile Glu Glu His Ser Trp Ala His Arg Ala Phe Ala Pro Phe Arg Leu 355 360 365 Ala His Ala Leu Leu Ala Ala Leu Ala Pro Ala Arg Thr Asp Gly Gly 370 375 380 Gly Gly Gly Ser Ile Pro Ala Ala Gln Ser Ala Thr Glu Ala Arg Gly 385 390 395 400 Ala Glu Pro Thr Ala Gly Ile His Trp Tyr Ser Gln Leu Leu Tyr His 405 410 415 Ile Gly Thr Trp Leu Leu Asp Ser Glu Thr Met His Pro Leu Gly Met 420 425 430 Ala Val Lys Ser Ser 435 21 418 PRT Brachydanio rerio 21 Met Arg Leu Leu Thr Arg Val Leu Leu Val Ser Leu Leu Thr Leu Ser 1 5 10 15 Leu Val Val Ser Gly Leu Ala Cys Gly Pro Gly Arg Gly Tyr Gly Arg 20 25 30 Arg Arg His Pro Lys Lys Leu Thr Pro Leu Ala Tyr Lys Gln Phe Ile 35 40 45 Pro Asn Val Ala Glu Lys Thr Leu Gly Ala Ser Gly Arg Tyr Glu Gly 50 55 60 Lys Ile Thr Arg Asn Ser Glu Arg Phe Lys Glu Leu Thr Pro Asn Tyr 65 70 75 80 Asn Pro Asp Ile Ile Phe Lys Asp Glu Glu Asn Thr Gly Ala Asp Arg 85 90 95 Leu Met Thr Gln Arg Cys Lys Asp Lys Leu Asn Ser Leu Ala Ile Ser 100 105 110 Val Met Asn His Trp Pro Gly Val Lys Leu Arg Val Thr Glu Gly Trp 115 120 125 Asp Glu Asp Gly His His Phe Glu Glu Ser Leu His Tyr Glu Gly Arg 130 135 140 Ala Val Asp Ile Thr Thr Ser Asp Arg Asp Lys Ser Lys Tyr Gly Thr 145 150 155 160 Leu Ser Arg Leu Ala Val Glu Ala Gly Phe Asp Trp Val Tyr Tyr Glu 165 170 175 Ser Lys Ala His Ile His Cys Ser Val Lys Ala Glu Asn Ser Val Ala 180 185 190 Ala Lys Ser Gly Gly Cys Phe Pro Gly Ser Ala Leu Val Ser Leu Gln 195 200 205 Asp Gly Gly Gln Lys Ala Val Lys Asp Leu Asn Pro Gly Asp Lys Val 210 215 220 Leu Ala Ala Asp Ser Ala Gly Asn Leu Val Phe Ser Asp Phe Ile Met 225 230 235 240 Phe Thr Asp Arg Asp Ser Thr Thr Arg Arg Val Phe Tyr Val Ile Glu 245 250 255 Thr Gln Glu Pro Val Glu Lys Ile Thr Leu Thr Ala Ala His Leu Leu 260 265 270 Phe Val Leu Asp Asn Ser Thr Glu Asp Leu His Thr Met Thr Ala Ala 275 280 285 Tyr Ala Ser Ser Val Arg Ala Gly Gln Lys Val Met Val Val Asp Asp 290 295 300 Ser Gly Gln Leu Lys Ser Val Ile Val Gln Arg Ile Tyr Thr Glu Glu 305 310 315 320 Gln Arg Gly Ser Phe Ala Pro Val Thr Ala His Gly Thr Ile Val Val 325 330 335 Asp Arg Ile Leu Ala Ser Cys Tyr Ala Val Ile Glu Asp Gln Gly Leu 340 345 350 Ala His Leu Ala Phe Ala Pro Ala Arg Leu Tyr Tyr Tyr Val Ser Ser 355 360 365 Phe Leu Ser Pro Lys Thr Pro Ala Val Gly Pro Met Arg Leu Tyr Asn 370 375 380 Arg Arg Gly Ser Thr Gly Thr Pro Gly Ser Cys His Gln Met Gly Thr 385 390 395 400 Trp Leu Leu Asp Ser Asn Met Leu His Pro Leu Gly Met Ser Val Asn 405 410 415 Ser Ser 22 475 PRT Homo sapiens Xaa may be any amino acid 22 Met Leu Leu Leu Ala Arg Cys Leu Leu Leu Val Leu Val Ser Ser Leu 1 5 10 15 Leu Val Cys Ser Gly Leu Ala Cys Gly Pro Gly Arg Gly Phe Gly Lys 20 25 30 Arg Arg His Pro Lys Lys Leu Thr Pro Leu Ala Tyr Lys Gln Phe Ile 35 40 45 Pro Asn Val Ala Glu Lys Thr Leu Gly Ala Ser Gly Arg Tyr Glu Gly 50 55 60 Lys Ile Ser Arg Asn Ser Glu Arg Phe Lys Glu Leu Thr Pro Asn Tyr 65 70 75 80 Asn Pro Asp Ile Ile Phe Lys Asp Glu Glu Asn Thr Gly Ala Asp Arg 85 90 95 Leu Met Thr Gln Arg Cys Lys Asp Lys Leu Asn Ala Leu Ala Ile Ser 100 105 110 Val Met Asn Gln Trp Pro Gly Val Lys Leu Arg Val Thr Glu Gly Trp 115 120 125 Asp Glu Asp Gly His His Ser Glu Glu Ser Leu His Tyr Glu Gly Arg 130 135 140 Ala Val Asp Ile Thr Thr Ser Asp Arg Asp Arg Ser Lys Tyr Gly Met 145 150 155 160 Leu Ala Arg Leu Ala Val Glu Ala Gly Phe Asp Trp Val Tyr Tyr Glu 165 170 175 Ser Lys Ala His Ile His Cys Ser Val Lys Ala Glu Asn Ser Val Ala 180 185 190 Ala Lys Ser Gly Gly Cys Phe Pro Gly Ser Ala Thr Val His Leu Glu 195 200 205 Gln Gly Gly Thr Lys Leu Val Lys Asp Leu Ser Pro Gly Asp Arg Val 210 215 220 Leu Ala Ala Asp Asp Gln Gly Arg Leu Leu Tyr Ser Asp Phe Leu Thr 225 230 235 240 Phe Leu Asp Arg Asp Asp Gly Ala Lys Lys Val Phe Tyr Val Ile Glu 245 250 255 Thr Arg Glu Pro Arg Glu Arg Leu Leu Leu Thr Ala Ala His Leu Leu 260 265 270 Phe Val Ala Pro His Asn Asp Ser Ala Thr Gly Glu Pro Glu Ala Ser 275 280 285 Ser Gly Ser Gly Pro Pro Ser Gly Gly Ala Leu Gly Pro Arg Ala Leu 290 295 300 Phe Ala Ser Arg Val Arg Pro Gly Gln Arg Val Tyr Val Val Ala Glu 305 310 315 320 Arg Asp Gly Asp Arg Arg Leu Leu Pro Ala Ala Val His Ser Val Thr 325 330 335 Leu Ser Glu Glu Ala Ala Gly Ala Tyr Ala Pro Leu Thr Ala Gln Gly 340 345 350 Thr Ile Leu Ile Asn Arg Val Leu Ala Ser Cys Tyr Ala Val Ile Glu 355 360 365 Glu His Ser Trp Ala His Arg Ala Phe Ala Pro Phe Arg Leu Ala His 370 375 380 Ala Leu Leu Ala Ala Leu Ala Pro Ala Arg Thr Asp Arg Gly Gly Asp 385 390 395 400 Ser Gly Gly Gly Asp Arg Gly Gly Gly Gly Gly Arg Val Ala Leu Thr 405 410 415 Ala Pro Gly Ala Ala Asp Ala Pro Gly Ala Gly Ala Thr Ala Gly Ile 420 425 430 His Trp Tyr Ser Gln Leu Leu Tyr Gln Ile Gly Thr Trp Leu Leu Asp 435 440 445 Ser Glu Ala Leu His Pro Leu Gly Met Ala Val Lys Ser Ser Xaa Ser 450 455 460 Arg Gly Ala Gly Gly Gly Ala Arg Glu Gly Ala 465 470 475 23 411 PRT Homo sapiens 23 Met Ser Pro Ala Arg Leu Arg Pro Arg Leu His Phe Cys Leu Val Leu 1 5 10 15 Leu Leu Leu Leu Val Val Pro Ala Ala Trp Gly Cys Gly Pro Gly Arg 20 25 30 Val Val Gly Ser Arg Arg Arg Pro Pro Arg Lys Leu Val Pro Leu Ala 35 40 45 Tyr Lys Gln Phe Ser Pro Asn Val Pro Glu Lys Thr Leu Gly Ala Ser 50 55 60 Gly Arg Tyr Glu Gly Lys Ile Ala Arg Ser Ser Glu Arg Phe Lys Glu 65 70 75 80 Leu Thr Pro Asn Tyr Asn Pro Asp Ile Ile Phe Lys Asp Glu Glu Asn 85 90 95 Thr Gly Ala Asp Arg Leu Met Thr Gln Arg Cys Lys Asp Arg Leu Asn 100 105 110 Ser Leu Ala Ile Ser Val Met Asn Gln Trp Pro Gly Val Lys Leu Arg 115 120 125 Val Thr Glu Gly Trp Asp Glu Asp Gly His His Ser Glu Glu Ser Leu 130 135 140 His Tyr Glu Gly Arg Ala Val Asp Ile Thr Thr Ser Asp Arg Asp Arg 145 150 155 160 Asn Lys Tyr Gly Leu Leu Ala Arg Leu Ala Val Glu Ala Gly Phe Asp 165 170 175 Trp Val Tyr Tyr Glu Ser Lys Ala His Val His Cys Ser Val Lys Ser 180 185 190 Glu His Ser Ala Ala Ala Lys Thr Gly Gly Cys Phe Pro Ala Gly Ala 195 200 205 Gln Val Arg Leu Glu Ser Gly Ala Arg Val Ala Leu Ser Ala Val Arg 210 215 220 Pro Gly Asp Arg Val Leu Ala Met Gly Glu Asp Gly Ser Pro Thr Phe 225 230 235 240 Ser Asp Val Leu Ile Phe Leu Asp Arg Glu Pro His Arg Leu Arg Ala 245 250 255 Phe Gln Val Ile Glu Thr Gln Asp Pro Pro Arg Arg Leu Ala Leu Thr 260 265 270 Pro Ala His Leu Leu Phe Thr Ala Asp Asn His Thr Glu Pro Ala Ala 275 280 285 Arg Phe Arg Ala Thr Phe Ala Ser His Val Gln Pro Gly Gln Tyr Val 290 295 300 Leu Val Ala Gly Val Pro Gly Leu Gln Pro Ala Arg Val Ala Ala Val 305 310 315 320 Ser Thr His Val Ala Leu Gly Ala Tyr Ala Pro Leu Thr Lys His Gly 325 330 335 Thr Leu Val Val Glu Asp Val Val Ala Ser Cys Phe Ala Ala Val Ala 340 345 350 Asp His His Leu Ala Gln Leu Ala Phe Trp Pro Leu Arg Leu Phe His 355 360 365 Ser Leu Ala Trp Gly Ser Trp Thr Pro Gly Glu Gly Val His Trp Tyr 370 375 380 Pro Gln Leu Leu Tyr Arg Leu Gly Arg Leu Leu Leu Glu Glu Gly Ser 385 390 395 400 Phe His Pro Leu Gly Met Ser Gly Ala Gly Ser 405 410 24 396 PRT Homo sapiens 24 Met Ala Leu Leu Thr Asn Leu Leu Pro Leu Cys Cys Leu Ala Leu Leu 1 5 10 15 Ala Leu Pro Ala Gln Ser Cys Gly Pro Gly Arg Gly Pro Val Gly Arg 20 25 30 Arg Arg Tyr Ala Arg Lys Gln Leu Val Pro Leu Leu Tyr Lys Gln Phe 35 40 45 Val Pro Gly Val Pro Glu Arg Thr Leu Gly Ala Ser Gly Pro Ala Glu 50 55 60 Gly Arg Val Ala Arg Gly Ser Glu Arg Phe Arg Asp Leu Val Pro Asn 65 70 75 80 Tyr Asn Pro Asp Ile Ile Phe Lys Asp Glu Glu Asn Ser Gly Ala Asp 85 90 95 Arg Leu Met Thr Glu Arg Cys Lys Glu Arg Val Asn Ala Leu Ala Ile 100 105 110 Ala Val Met Asn Met Trp Pro Gly Val Arg Leu Arg Val Thr Glu Gly 115 120 125 Trp Asp Glu Asp Gly His His Ala Gln Asp Ser Leu His Tyr Glu Gly 130 135 140 Arg Ala Leu Asp Ile Thr Thr Ser Asp Arg Asp Arg Asn Lys Tyr Gly 145 150 155 160 Leu Leu Ala Arg Leu Ala Val Glu Ala Gly Phe Asp Trp Val Tyr Tyr 165 170 175 Glu Ser Arg Asn His Val His Val Ser Val Lys Ala Asp Asn Ser Leu 180 185 190 Ala Val Arg Ala Gly Gly Cys Phe Pro Gly Asn Ala Thr Val Arg Leu 195 200 205 Trp Ser Gly Glu Arg Lys Gly Leu Arg Glu Leu His Arg Gly Asp Trp 210 215 220 Val Leu Ala Ala Asp Ala Ser Gly Arg Val Val Pro Thr Pro Val Leu 225 230 235 240 Leu Phe Leu Asp Arg Asp Leu Gln Arg Arg Ala Ser Phe Val Ala Val 245 250 255 Glu Thr Glu Trp Pro Pro Arg Lys Leu Leu Leu Thr Pro Trp His Leu 260 265 270 Val Phe Ala Ala Arg Gly Pro Ala Pro Ala Pro Gly Asp Phe Ala Pro 275 280 285 Val Phe Ala Arg Arg Leu Arg Ala Gly Asp Ser Val Leu Ala Pro Gly 290 295 300 Gly Asp Ala Leu Arg Pro Ala Arg Val Ala Arg Val Ala Arg Glu Glu 305 310 315 320 Ala Val Gly Val Phe Ala Pro Leu Thr Ala His Gly Thr Leu Leu Val 325 330 335 Asn Asp Val Leu Ala Ser Cys Tyr Ala Val Leu Glu Ser His Gln Trp 340 345 350 Ala His Arg Ala Phe Ala Pro Leu Arg Leu Leu His Ala Leu Gly Ala 355 360 365 Leu Leu Pro Gly Gly Ala Val Gln Pro Thr Gly Met His Trp Tyr Ser 370 375 380 Arg Leu Leu Tyr Arg Leu Ala Glu Glu Leu Leu Gly 385 390 395 25 416 PRT Brachydanio rerio 25 Met Asp Val Arg Leu His Leu Lys Gln Phe Ala Leu Leu Cys Phe Ile 1 5 10 15 Ser Leu Leu Leu Thr Pro Cys Gly Leu Ala Cys Gly Pro Gly Arg Gly 20 25 30 Tyr Gly Lys Arg Arg His Pro Lys Lys Leu Thr Pro Leu Ala Tyr Lys 35 40 45 Gln Phe Ile Pro Asn Val Ala Glu Lys Thr Leu Gly Ala Ser Gly Lys 50 55 60 Tyr Glu Gly Lys Ile Thr Arg Asn Ser Glu Arg Phe Lys Glu Leu Ile 65 70 75 80 Pro Asn Tyr Asn Pro Asp Ile Ile Phe Lys Asp Glu Glu Asn Thr Asn 85 90 95 Ala Asp Arg Leu Met Thr Lys Arg Cys Lys Asp Lys Leu Asn Ser Leu 100 105 110 Ala Ile Ser Val Met Asn His Trp Pro Gly Val Lys Leu Arg Val Thr 115 120 125 Glu Gly Trp Asp Glu Asp Gly His His Leu Glu Glu Ser Leu His Tyr 130 135 140 Glu Gly Arg Ala Val Asp Ile Thr Thr Ser Asp Arg Asp Lys Ser Lys 145 150 155 160 Tyr Gly Met Leu Ser Arg Leu Ala Val Glu Ala Gly Phe Asp Trp Val 165 170 175 Tyr Tyr Glu Ser Lys Ala His Ile His Cys Ser Val Lys Ala Glu Asn 180 185 190 Ser Val Ala Ala Lys Ser Gly Gly Cys Phe Pro Gly Ser Gly Thr Val 195 200 205 Thr Leu Gly Asp Gly Thr Arg Lys Pro Ile Lys Asp Leu Lys Val Gly 210 215 220 Asp Arg Val Leu Ala Ala Asp Glu Lys Gly Asn Val Leu Ile Ser Asp 225 230 235 240 Phe Ile Met Phe Ile Asp His Asp Pro Thr Thr Arg Arg Gln Phe Ile 245 250 255 Val Ile Glu Thr Ser Glu Pro Phe Thr Lys Leu Thr Leu Thr Ala Ala 260 265 270 His Leu Val Phe Val Gly Asn Ser Ser Ala Ala Ser Gly Ile Thr Ala 275 280 285 Thr Phe Ala Ser Asn Val Lys Pro Gly Asp Thr Val Leu Val Trp Glu 290 295 300 Asp Thr Cys Glu Ser Leu Lys Ser Val Thr Val Lys Arg Ile Tyr Thr 305 310 315 320 Glu Glu His Glu Gly Ser Phe Ala Pro Val Thr Ala His Gly Thr Ile 325 330 335 Ile Val Asp Gln Val Leu Ala Ser Cys Tyr Ala Val Ile Glu Asn His 340 345 350 Lys Trp Ala His Trp Ala Phe Ala Pro Val Arg Leu Cys His Lys Leu 355 360 365 Met Thr Trp Leu Phe Pro Ala Arg Glu Ser Asn Val Asn Phe Gln Glu 370 375 380 Asp Gly Ile His Trp Tyr Ser Asn Met Leu Phe His Ile Gly Ser Trp 385 390 395 400 Leu Leu Asp Arg Asp Ser Phe His Pro Leu Gly Ile Leu His Leu Ser 405 410 415 26 471 PRT Drosophilia sp. 26 Met Asp Asn His Ser Ser Val Pro Trp Ala Ser Ala Ala Ser Val Thr 1 5 10 15 Cys Leu Ser Leu Gly Cys Gln Met Pro Gln Phe Gln Phe Gln Phe Gln 20 25 30 Leu Gln Ile Arg Ser Glu Leu His Leu Arg Lys Pro Ala Arg Arg Thr 35 40 45 Gln Thr Met Arg His Ile Ala His Thr Gln Arg Cys Leu Ser Arg Leu 50 55 60 Thr Ser Leu Val Ala Leu Leu Leu Ile Val Leu Pro Met Val Phe Ser 65 70 75 80 Pro Ala His Ser Cys Gly Pro Gly Arg Gly Leu Gly Arg His Arg Ala 85 90 95 Arg Asn Leu Tyr Pro Leu Val Leu Lys Gln Thr Ile Pro Asn Leu Ser 100 105 110 Glu Tyr Thr Asn Ser Ala Ser Gly Pro Leu Glu Gly Val Ile Arg Arg 115 120 125 Asp Ser Pro Lys Phe Lys Asp Leu Val Pro Asn Tyr Asn Arg Asp Ile 130 135 140 Leu Phe Arg Asp Glu Glu Gly Thr Gly Ala Asp Gly Leu Met Ser Lys 145 150 155 160 Arg Cys Lys Glu Lys Leu Asn Val Leu Ala Tyr Ser Val Met Asn Glu 165 170 175 Trp Pro Gly Ile Arg Leu Leu Val Thr Glu Ser Trp Asp Glu Asp Tyr 180 185 190 His His Gly Gln Glu Ser Leu His Tyr Glu Gly Arg Ala Val Thr Ile 195 200 205 Ala Thr Ser Asp Arg Asp Gln Ser Lys Tyr Gly Met Leu Ala Arg Leu 210 215 220 Ala Val Glu Ala Gly Phe Asp Trp Val Ser Tyr Val Ser Arg Arg His 225 230 235 240 Ile Tyr Cys Ser Val Lys Ser Asp Ser Ser Ile Ser Ser His Val His 245 250 255 Gly Cys Phe Thr Pro Glu Ser Thr Ala Leu Leu Glu Ser Gly Val Arg 260 265 270 Lys Pro Leu Gly Glu Leu Ser Ile Gly Asp Arg Val Leu Ser Met Thr 275 280 285 Ala Asn Gly Gln Ala Val Tyr Ser Glu Val Ile Leu Phe Met Asp Arg 290 295 300 Asn Leu Glu Gln Met Gln Asn Phe Val Gln Leu His Thr Asp Gly Gly 305 310 315 320 Ala Val Leu Thr Val Thr Pro Ala His Leu Val Ser Val Trp Gln Pro 325 330 335 Glu Ser Gln Lys Leu Thr Phe Val Phe Ala His Arg Ile Glu Glu Lys 340 345 350 Asn Gln Val Leu Val Arg Asp Val Glu Thr Gly Glu Leu Arg Pro Gln 355 360 365 Arg Val Val Lys Leu Gly Ser Val Arg Ser Lys Gly Val Val Ala Pro 370 375 380 Leu Thr Arg Glu Gly Thr Ile Val Val Asn Ser Val Ala Ala Ser Cys 385 390 395 400 Tyr Ala Val Ile Asn Ser Gln Ser Leu Ala His Trp Gly Leu Ala Pro 405 410 415 Met Arg Leu Leu Ser Thr Leu Glu Ala Trp Leu Pro Ala Lys Glu Gln 420 425 430 Leu His Ser Ser Pro Lys Val Val Ser Ser Ala Gln Gln Gln Asn Gly 435 440 445 Ile His Trp Tyr Ala Asn Ala Leu Tyr Lys Val Lys Asp Tyr Val Leu 450 455 460 Pro Gln Ser Trp Arg His Asp 465 470 27 39 DNA Artificial Sequence Description of Artificial Sequence Primer 27 ggcgatgacg atgacaaatt cggaccgggc agggggttc 39 28 39 DNA Artificial Sequence Description of Artificial Sequence Primer 28 ggcgatgacg atgacaaaat aggaccgggc agggggttc 39 29 42 DNA Artificial Sequence Description of Artificial Sequence Primer 29 ggcgatgacg atgacaaaat gggcccgggc agggggttcg gg 42 30 47 DNA Artificial Sequence Description of Artificial Sequence Primer 30 gcggcgatga cgatgacaaa atcatcggac cgggcagggg gttcggg 47 31 49 DNA Artificial Sequence Description of Artificial Sequence Primer 31 gagtcatcag cctcccgatt ttgcgcacac cgagttctct gctttcacc 49 

What is claimed is:
 1. An isolated protein comprising an N-terminal amino acid and a C-terminal amino acid, wherein the protein is selected from the group consisting of: (a) a protein with an N-terminal cysteine that is appended with at least one hydrophobic moiety; (b) a protein with an N-terminal amino acid that is not a cysteine appended with at least one hydrophobic moiety; and (c) a protein with at least one hydrophobic moiety substituted for the N-terminal amino acid, wherein the protein is a hedgehog protein obtainable from a vertebrate source.
 2. The prorein of claim 1 wherein the hydrophobic moiety is a lipid moiety.
 3. The protein of claim 1, where the N-terminal amino acid is a functional derivative of a cysteine.
 4. The protein of claim 1, wherein the hedgehog protein is obtainable from a human or rat.
 5. The protein of claim 1, wherein the hedgehog protein is selected from the group consisting of Sonic, Indian, and Desert hedgehog.
 6. The protein of claim 5, wherein the hedgehog protein is missing between 1 and about 10 amino acids from the C-terminus thereof, when compared to a wild-type hedgehog protein.
 7. The protein of claim 1, further comprising a vesicle in contact with the hydrophobic moiety.
 8. The protein of claim 7, wherein the vesicle is selected from the group consisting of a cell membrane, a micelle, and a liposome.
 9. The protein of claim 1, wherein the hedgehog protein has an amino acid sequence according to any one of SEQ ID NOS: 1-4.
 10. An isolated protein comprising an N-terminal amino acid and a C-terminal amino acid, wherein the protein is selected from the group consisting of: (a) a protein with an N-terminal cysteine that is appended with at least one hydrophobic moiety; (b) a protein with an N-terminal amino-acid that is not a cysteine appended with at least one hydrophobic moiety; and (c) a protein with at least one hydrophobic moiety substituted for the N-terminal amino acid; wherein the protein binds to patched and has at least 80% amino acid identity to a hedgehog amino acid sequence selected from the group consisting of SEQ ID No:5, SEQ ID No:6, SEQ ID No:7, SEQ ID No:8, SEQ ID No:9, SEQ ID No:10, SEQ ID No:11, SEQ ID No:12, SEQ ID No:13 and SEQ ID No:14, or an extracellular fragment thereof.
 11. A protein of claim 1 or 10 wherein the at least one hydrophobic moiety is selected from the group consisting of: a myristoyl group, a palmitoyl group, a stearoyl group, an arachidoyl group, an acetyl group, a butyryl group, a hexanoyl group, an octanoyl group, a decanoyl group, a lauroyl group, a palmitoleoyl group, a behenoyl group, and a lignoceroyl group.
 12. An isolated hedgehog protein modified with one or more lipophilic moieties with the proviso that, in the instance wherein the hedgehog polypeptide is the mature N-terminal proteolytic fragment of a hedgehog protein, the lipophilic moiety is other than a sterol at the C-terminal residue, which hedgehog polypeptide binds to patched and has an amino acid sequence at least 80 percent identical to a hedgehog amino acid sequence selected from the group consisting of SEQ ID No:5, SEQ ID No:6, SEQ ID No:7, SEQ ID No:8, SEQ ID No:9, SEQ ID No:10, SEQ ID No:11, SEQ ID No:12, SEQ ID No:13 and SEQ ID No:14, or an extracellular fragment thereof.
 13. The hedgehog polypeptide of claim 12, which polypeptide is provided as a purified protein preparation.
 14. The hedgehog polypeptide of claim 12, which polypeptide is provided as a pharmaceutical preparation.
 15. The hedgehog polypeptide of claim 12, wherein the lipophilic moieties are selected from the group consisting of fatty acids, lipids, esters, alcohols, cage structures, and aromatic hydrocarbons.
 16. The hedgehog polypeptide of claim 12, wherein the lipophilic moiety or moieties potentiate the biological activity of the polypeptide relative to the unmodified hedgehog polypeptide.
 17. An isolated protein comprising a hedgehog amino acid sequence derivatived with at least one fatty acid moiety, which hedgehog amino acid sequence binds to patched and is at least 80 percent identical to a hedgehog amino acid sequence selected from the group consisting of SEQ ID No:5, SEQ ID No:6, SEQ ID No:7, SEQ ID No:8, SEQ ID No:9, SEQ ID No:10, SEQ ID No:11, SEQ ID No:12, SEQ ID No:13 and SEQ ID No:14, or an extracellular fragment thereof.
 18. The protein of claim 17, wherein the lipid moiety is fatty acid selected from saturated and unsaturated fatty acids having between 2 and 24 carbon atoms.
 19. The protein of claim 17, wherein each fatty acid moiety is independently selected from the group consisting of a myristoyl group, a palmitoyl group, a stearoyl group, an arachidoyl group, an acetyl group, a butytyl group, a hexanoyl group, an octanoyl group, a decanoyl group, a lauroyl group, a palmitoleoyl group, a behenoyl group, and a lignoceroyl group.
 20. The protein of claim 17, wherein said fatty acid moiety is covalently linked through a cysteine sidechain of the hedgehog amino acid sequence.
 21. A method for modifying a physico-chemical property of a protein, comprising introducing at least one hydrophobic moiety to an N-terminal cysteine of the protein or to a functional equivalent of the N-terminal cysteine, wherein the protein is a hedgehog protein.
 22. The method of claim 21, further comprising contacting the hydrophobic moiety with a vesicle.
 23. The method of claim 22, wherein the step of contacting comprises contacting with a vesicle selected from the group consisting of a cell membrane, liposome and micelle.
 24. The method of claim 21, wherein the hydrophobic moiety is either a lipid moiety selected from saturated and unsaturated fatty acids having between 2 and 24 carbon atoms or is a hydrophobic protein.
 25. The method of claim 21, wherein the hedgehog protein is selected from the group consisting of Sonic, Indian and Desert hedgehog.
 26. The method of claim 21, wherein the hedgehog has an amino acid sequence according to any one of SEQ ID NOS: 1-4.
 27. A modified protein, produced by the method of claim
 21. 